From b24f83277f7b89163fff91254fb8aea647f891a4 Mon Sep 17 00:00:00 2001 From: Alexander Sebastian Hauser Date: Mon, 10 Aug 2015 15:48:05 +0200 Subject: [PATCH 1/2] Representative structures endogenous ligand updates and new constructs --- structure_data/constructs/2I37.yaml | 2 ++ structure_data/constructs/2YCZ.yaml | 2 ++ structure_data/constructs/4XNW.yaml | 2 ++ structure_data/constructs/4XT3.yaml | 2 ++ structure_data/constructs/4YAY.yaml | 2 ++ structure_data/constructs/4Z34.yaml | 2 ++ structure_data/pdb_structures/2I37.yaml | 2 ++ structure_data/pdb_structures/2RH1.yaml | 21 ++++++++----- structure_data/pdb_structures/2YCZ.yaml | 2 ++ structure_data/pdb_structures/3ODU.yaml | 4 +++ structure_data/pdb_structures/3PBL.yaml | 3 ++ structure_data/pdb_structures/3RZE.yaml | 3 ++ structure_data/pdb_structures/3UON.yaml | 3 ++ structure_data/pdb_structures/3V2Y.yaml | 3 ++ structure_data/pdb_structures/3VW7.yaml | 3 ++ structure_data/pdb_structures/4BUO.yaml | 3 ++ structure_data/pdb_structures/4DJH.yaml | 3 ++ structure_data/pdb_structures/4DKL.yaml | 8 +++++ structure_data/pdb_structures/4EA3.yaml | 3 ++ structure_data/pdb_structures/4EIY.yaml | 3 ++ structure_data/pdb_structures/4EJ4.yaml | 8 +++++ structure_data/pdb_structures/4IAR.yaml | 3 ++ structure_data/pdb_structures/4IB4.yaml | 3 ++ structure_data/pdb_structures/4JKV.yaml | 3 ++ structure_data/pdb_structures/4K5Y.yaml | 3 ++ structure_data/pdb_structures/4L6R.yaml | 3 ++ structure_data/pdb_structures/4LDE.yaml | 3 ++ structure_data/pdb_structures/4MBS.yaml | 11 +++++++ structure_data/pdb_structures/4MQS.yaml | 3 ++ structure_data/pdb_structures/4N6H.yaml | 8 +++++ structure_data/pdb_structures/4OO9.yaml | 3 ++ structure_data/pdb_structures/4OR2.yaml | 3 ++ structure_data/pdb_structures/4PHU.yaml | 3 ++ structure_data/pdb_structures/4PXZ.yaml | 3 ++ structure_data/pdb_structures/4S0V.yaml | 4 +++ structure_data/pdb_structures/4U15.yaml | 3 ++ structure_data/pdb_structures/4XNW.yaml | 2 ++ structure_data/pdb_structures/4XT3.yaml | 2 ++ structure_data/pdb_structures/4YAY.yaml | 41 +++++++++++++++++++++++++ structure_data/pdb_structures/4Z34.yaml | 2 ++ 40 files changed, 183 insertions(+), 7 deletions(-) create mode 100644 structure_data/constructs/2I37.yaml create mode 100644 structure_data/constructs/2YCZ.yaml create mode 100644 structure_data/constructs/4XNW.yaml create mode 100644 structure_data/constructs/4XT3.yaml create mode 100644 structure_data/constructs/4YAY.yaml create mode 100644 structure_data/constructs/4Z34.yaml create mode 100644 structure_data/pdb_structures/2I37.yaml create mode 100644 structure_data/pdb_structures/2YCZ.yaml create mode 100644 structure_data/pdb_structures/4XNW.yaml create mode 100644 structure_data/pdb_structures/4XT3.yaml create mode 100644 structure_data/pdb_structures/4YAY.yaml create mode 100644 structure_data/pdb_structures/4Z34.yaml diff --git a/structure_data/constructs/2I37.yaml b/structure_data/constructs/2I37.yaml new file mode 100644 index 00000000..d8a61ba6 --- /dev/null +++ b/structure_data/constructs/2I37.yaml @@ -0,0 +1,2 @@ +name: 2i37 +protein: opsd_bovin \ No newline at end of file diff --git a/structure_data/constructs/2YCZ.yaml b/structure_data/constructs/2YCZ.yaml new file mode 100644 index 00000000..9d3c1f46 --- /dev/null +++ b/structure_data/constructs/2YCZ.yaml @@ -0,0 +1,2 @@ +name: 2ycz +protein: adrb1_melga \ No newline at end of file diff --git a/structure_data/constructs/4XNW.yaml b/structure_data/constructs/4XNW.yaml new file mode 100644 index 00000000..ea99b94f --- /dev/null +++ b/structure_data/constructs/4XNW.yaml @@ -0,0 +1,2 @@ +name: 4xnw +protein: p2ry1_human \ No newline at end of file diff --git a/structure_data/constructs/4XT3.yaml b/structure_data/constructs/4XT3.yaml new file mode 100644 index 00000000..dd98df20 --- /dev/null +++ b/structure_data/constructs/4XT3.yaml @@ -0,0 +1,2 @@ +name: 4xt3 +protein: us28_hcmva \ No newline at end of file diff --git a/structure_data/constructs/4YAY.yaml b/structure_data/constructs/4YAY.yaml new file mode 100644 index 00000000..1efb636c --- /dev/null +++ b/structure_data/constructs/4YAY.yaml @@ -0,0 +1,2 @@ +name: 4yay +protein: agtr1_human \ No newline at end of file diff --git a/structure_data/constructs/4Z34.yaml b/structure_data/constructs/4Z34.yaml new file mode 100644 index 00000000..4ed9aada --- /dev/null +++ b/structure_data/constructs/4Z34.yaml @@ -0,0 +1,2 @@ +name: 4z34 +protein: lpar1_human \ No newline at end of file diff --git a/structure_data/pdb_structures/2I37.yaml b/structure_data/pdb_structures/2I37.yaml new file mode 100644 index 00000000..d8a61ba6 --- /dev/null +++ b/structure_data/pdb_structures/2I37.yaml @@ -0,0 +1,2 @@ +name: 2i37 +protein: opsd_bovin \ No newline at end of file diff --git a/structure_data/pdb_structures/2RH1.yaml b/structure_data/pdb_structures/2RH1.yaml index 333ca335..415356c2 100644 --- a/structure_data/pdb_structures/2RH1.yaml +++ b/structure_data/pdb_structures/2RH1.yaml @@ -1,16 +1,23 @@ # PDB data + pdb: 2RH1 -resolution: 2.4 -publication_date: 2007-10-30 -pubmed_id: 17962520 +publication_date: '2007-10-30' +pubmed_id: '17962520' +resolution: '2.4' # Structure annotations -ligand: [{name: Carazolol, role: Inverse agonist}] -state: Inactive -preferred_chain: A + g_protein: None +ligand: +- {name: Carazolol, role: Inverse agonist} +endogenous_ligand: +- {name: noradrenaline, id: 484} +preferred_chain: +state: Inactive +representative: true + +# Structure annotations -# Other data construct: b2ar-t4l segments: TM1: [29,60] diff --git a/structure_data/pdb_structures/2YCZ.yaml b/structure_data/pdb_structures/2YCZ.yaml new file mode 100644 index 00000000..9d3c1f46 --- /dev/null +++ b/structure_data/pdb_structures/2YCZ.yaml @@ -0,0 +1,2 @@ +name: 2ycz +protein: adrb1_melga \ No newline at end of file diff --git a/structure_data/pdb_structures/3ODU.yaml b/structure_data/pdb_structures/3ODU.yaml index 9c23f9b6..c65a76da 100644 --- a/structure_data/pdb_structures/3ODU.yaml +++ b/structure_data/pdb_structures/3ODU.yaml @@ -10,8 +10,12 @@ resolution: '2.50' g_protein: None ligand: - {name: IT1t, role: Antagonist} +endogenous_ligand: +- {name: CXCL12, id: 4358} +- {name: SDF-1β, id: 845} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/3PBL.yaml b/structure_data/pdb_structures/3PBL.yaml index 564bb5b9..ba17db58 100644 --- a/structure_data/pdb_structures/3PBL.yaml +++ b/structure_data/pdb_structures/3PBL.yaml @@ -10,8 +10,11 @@ resolution: '2.89' g_protein: None ligand: - {name: Eticlopride, role: Antagonist} +endogenous_ligand: +- {name: Dopamine, id: 940} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/3RZE.yaml b/structure_data/pdb_structures/3RZE.yaml index b01d1475..853d9972 100644 --- a/structure_data/pdb_structures/3RZE.yaml +++ b/structure_data/pdb_structures/3RZE.yaml @@ -10,8 +10,11 @@ resolution: '3.10' g_protein: None ligand: - {name: 'Doxepin (E,Z)', role: Antagonist} +endogenous_ligand: +- {name: Histamine, id: 1204} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/3UON.yaml b/structure_data/pdb_structures/3UON.yaml index 04303b5c..0492607b 100644 --- a/structure_data/pdb_structures/3UON.yaml +++ b/structure_data/pdb_structures/3UON.yaml @@ -10,8 +10,11 @@ resolution: '3.00' g_protein: None ligand: - {name: QNB, role: Antagonist} +endogenous_ligand: +- {name: Acetylcholine, id: 294} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/3V2Y.yaml b/structure_data/pdb_structures/3V2Y.yaml index 2a0f1f7b..3548bb9e 100644 --- a/structure_data/pdb_structures/3V2Y.yaml +++ b/structure_data/pdb_structures/3V2Y.yaml @@ -10,8 +10,11 @@ resolution: '2.80' g_protein: None ligand: - {name: Spingolipid mimic, role: Antagonist} +endogenous_ligand: +- {name: Sphingosine-1-phosphate, id: 911} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/3VW7.yaml b/structure_data/pdb_structures/3VW7.yaml index bbde6327..0c23b595 100644 --- a/structure_data/pdb_structures/3VW7.yaml +++ b/structure_data/pdb_structures/3VW7.yaml @@ -10,8 +10,11 @@ resolution: '2.20' g_protein: None ligand: - {name: Vorapaxar, role: Antagonist} +endogenous_ligand: +- {name: Thrombin, id: 4453} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4BUO.yaml b/structure_data/pdb_structures/4BUO.yaml index be025781..3c4f2f83 100644 --- a/structure_data/pdb_structures/4BUO.yaml +++ b/structure_data/pdb_structures/4BUO.yaml @@ -10,8 +10,11 @@ resolution: '2.75' g_protein: None ligand: - {name: NTS(8-13), role: Agonist} +endogenous_ligand: +- {name: Neurotensin, id: 1579} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4DJH.yaml b/structure_data/pdb_structures/4DJH.yaml index f967c55d..11c92010 100644 --- a/structure_data/pdb_structures/4DJH.yaml +++ b/structure_data/pdb_structures/4DJH.yaml @@ -10,8 +10,11 @@ resolution: '2.90' g_protein: None ligand: - {name: JDTic, role: Antagonist} +endogenous_ligand: +- {name: Dynorphin A, id: 1620} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4DKL.yaml b/structure_data/pdb_structures/4DKL.yaml index 95cbf0d2..058bee23 100644 --- a/structure_data/pdb_structures/4DKL.yaml +++ b/structure_data/pdb_structures/4DKL.yaml @@ -10,8 +10,16 @@ resolution: '2.80' g_protein: None ligand: - {name: Morphinan, role: Antagonist} +endogenous_ligand: +- {name: β-endorphin, id: 1643} +- {name: dynorphin A, id: 1620} +- {name: dynorphin B, id: 1622} +- {name: endomorphin-1, id: 1623} +- {name: Leo-enkephalin, id: 1613} +- {name: Met-enkephalin, id: 1614} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4EA3.yaml b/structure_data/pdb_structures/4EA3.yaml index fb37b5e3..658074b4 100644 --- a/structure_data/pdb_structures/4EA3.yaml +++ b/structure_data/pdb_structures/4EA3.yaml @@ -10,8 +10,11 @@ resolution: '3.01' g_protein: None ligand: - {name: Compound 24, role: Antagonist} +endogenous_ligand: +- {name: nociceptin/orphanin FQ, id: 1681} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4EIY.yaml b/structure_data/pdb_structures/4EIY.yaml index a60de685..6b6bb2cf 100644 --- a/structure_data/pdb_structures/4EIY.yaml +++ b/structure_data/pdb_structures/4EIY.yaml @@ -10,8 +10,11 @@ resolution: '1.80' g_protein: None ligand: - {name: ZM241385, role: Antagonist} +endogenous_ligand: +- {name: adenosine diphosphate, id: 1712} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4EJ4.yaml b/structure_data/pdb_structures/4EJ4.yaml index cc7ade1a..b8ff313e 100644 --- a/structure_data/pdb_structures/4EJ4.yaml +++ b/structure_data/pdb_structures/4EJ4.yaml @@ -10,8 +10,16 @@ resolution: '3.40' g_protein: None ligand: - {name: Naltrindole, role: Antagonist} +endogenous_ligand: +- {name: β-endorphin, id: 1643} +- {name: dynorphin A, id: 1620} +- {name: dynorphin B, id: 1622} +- {name: endomorphin-1, id: 1623} +- {name: Leo-enkephalin, id: 1613} +- {name: Met-enkephalin, id: 1614} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4IAR.yaml b/structure_data/pdb_structures/4IAR.yaml index 5bbe9d85..566838a6 100644 --- a/structure_data/pdb_structures/4IAR.yaml +++ b/structure_data/pdb_structures/4IAR.yaml @@ -10,8 +10,11 @@ resolution: '2.70' g_protein: None ligand: - {name: Ergotamine, role: Agonist} +endogenous_ligand: +- {name: Serotonin, id: 5} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4IB4.yaml b/structure_data/pdb_structures/4IB4.yaml index ec2bb3f6..a6fdd27b 100644 --- a/structure_data/pdb_structures/4IB4.yaml +++ b/structure_data/pdb_structures/4IB4.yaml @@ -10,8 +10,11 @@ resolution: '2.70' g_protein: None ligand: - {name: Ergotamine, role: Agonist} +endogenous_ligand: +- {name: Serotonin, id: 5} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4JKV.yaml b/structure_data/pdb_structures/4JKV.yaml index faf3906f..9a040f27 100644 --- a/structure_data/pdb_structures/4JKV.yaml +++ b/structure_data/pdb_structures/4JKV.yaml @@ -10,8 +10,11 @@ resolution: '2.45' g_protein: None ligand: - {name: LY2940680, role: Antagonist} +endogenous_ligand: +- {name: nan, id: nan} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4K5Y.yaml b/structure_data/pdb_structures/4K5Y.yaml index b51f8a60..c06b7a4d 100644 --- a/structure_data/pdb_structures/4K5Y.yaml +++ b/structure_data/pdb_structures/4K5Y.yaml @@ -10,8 +10,11 @@ resolution: '2.98' g_protein: None ligand: - {name: CP-376395, role: Antagonist} +endogenous_ligand: +- {name: Corticotropin-releasing hormone, id: 912} preferred_chain: C state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4L6R.yaml b/structure_data/pdb_structures/4L6R.yaml index 1b241003..50303562 100644 --- a/structure_data/pdb_structures/4L6R.yaml +++ b/structure_data/pdb_structures/4L6R.yaml @@ -10,8 +10,11 @@ resolution: '3.30' g_protein: None ligand: - {name: '', role: N/A} +endogenous_ligand: +- {name: Glucagon, id: 1136} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4LDE.yaml b/structure_data/pdb_structures/4LDE.yaml index d97d1a52..a519fe12 100644 --- a/structure_data/pdb_structures/4LDE.yaml +++ b/structure_data/pdb_structures/4LDE.yaml @@ -10,8 +10,11 @@ resolution: '2.79' g_protein: Nanobody ligand: - {name: BI-167107, role: Agonist} +endogenous_ligand: +- {name: noradrenaline, id: 484} preferred_chain: A state: Active +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4MBS.yaml b/structure_data/pdb_structures/4MBS.yaml index 70c6ab91..6fa3df3b 100644 --- a/structure_data/pdb_structures/4MBS.yaml +++ b/structure_data/pdb_structures/4MBS.yaml @@ -10,8 +10,19 @@ resolution: '2.71' g_protein: None ligand: - {name: Maraviroc, role: Antagonist} +endogenous_ligand: +- {name: CCL11, id: 769} +- {name: CCL14, id: 753} +- {name: CCL16, id: 1272} +- {name: CCL2, id: 771} +- {name: CCL3, id: 756} +- {name: CCL4, id: 757} +- {name: CCL5, id: 758} +- {name: CCL7, id: 759} +- {name: CCL8, id: 772} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4MQS.yaml b/structure_data/pdb_structures/4MQS.yaml index 07889e20..75cdd264 100644 --- a/structure_data/pdb_structures/4MQS.yaml +++ b/structure_data/pdb_structures/4MQS.yaml @@ -10,8 +10,11 @@ resolution: '3.50' g_protein: Nanobody ligand: - {name: Iperoxo, role: Agonist} +endogenous_ligand: +- {name: Acetylcholine, id: 294} preferred_chain: A state: Active +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4N6H.yaml b/structure_data/pdb_structures/4N6H.yaml index 25080d62..2cb3db0b 100644 --- a/structure_data/pdb_structures/4N6H.yaml +++ b/structure_data/pdb_structures/4N6H.yaml @@ -10,8 +10,16 @@ resolution: '1.80' g_protein: None ligand: - {name: Naltrindole, role: Antagonist} +endogenous_ligand: +- {name: β-endorphin, id: 1643} +- {name: dynorphin A, id: 1620} +- {name: dynorphin B, id: 1622} +- {name: endomorphin-1, id: 1623} +- {name: Leo-enkephalin, id: 1613} +- {name: Met-enkephalin, id: 1614} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4OO9.yaml b/structure_data/pdb_structures/4OO9.yaml index d776f4ac..07ecfdf5 100644 --- a/structure_data/pdb_structures/4OO9.yaml +++ b/structure_data/pdb_structures/4OO9.yaml @@ -10,8 +10,11 @@ resolution: '2.60' g_protein: None ligand: - {name: Mavoglurant, role: NAM} +endogenous_ligand: +- {name: L-glutamic acid, id: 1369} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4OR2.yaml b/structure_data/pdb_structures/4OR2.yaml index bfbea9cc..c923f796 100644 --- a/structure_data/pdb_structures/4OR2.yaml +++ b/structure_data/pdb_structures/4OR2.yaml @@ -10,8 +10,11 @@ resolution: '2.80' g_protein: None ligand: - {name: FITM, role: NAM} +endogenous_ligand: +- {name: L-glutamic acid, id: 1369} preferred_chain: A,B state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4PHU.yaml b/structure_data/pdb_structures/4PHU.yaml index 3cafbc8c..52db8a3b 100644 --- a/structure_data/pdb_structures/4PHU.yaml +++ b/structure_data/pdb_structures/4PHU.yaml @@ -10,8 +10,11 @@ resolution: '2.33' g_protein: None ligand: - {name: TAK-875, role: Agonist} +endogenous_ligand: +- {name: docosahexaenoic acid, id: 1051} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4PXZ.yaml b/structure_data/pdb_structures/4PXZ.yaml index 7363adee..18b1e3df 100644 --- a/structure_data/pdb_structures/4PXZ.yaml +++ b/structure_data/pdb_structures/4PXZ.yaml @@ -10,8 +10,11 @@ resolution: '2.50' g_protein: None ligand: - {name: 2MeSADP, role: Agonist} +endogenous_ligand: +- {name: adenosine diphosphate, id: 1712} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4S0V.yaml b/structure_data/pdb_structures/4S0V.yaml index ab1e368f..9a38c33c 100644 --- a/structure_data/pdb_structures/4S0V.yaml +++ b/structure_data/pdb_structures/4S0V.yaml @@ -10,8 +10,12 @@ resolution: '2.50' g_protein: None ligand: - {name: Suvorexant, role: Antagonist} +endogenous_ligand: +- {name: Orexin-A, id: 1697} +- {name: Orexin-B, id: 1699} preferred_chain: A state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4U15.yaml b/structure_data/pdb_structures/4U15.yaml index 5d56e6c3..4e64057e 100644 --- a/structure_data/pdb_structures/4U15.yaml +++ b/structure_data/pdb_structures/4U15.yaml @@ -10,8 +10,11 @@ resolution: '2.80' g_protein: None ligand: - {name: Tiotropium, role: Antagonist} +endogenous_ligand: +- {name: Acetylcholine, id: 294} preferred_chain: B state: Inactive +representative: true # Structure annotations diff --git a/structure_data/pdb_structures/4XNW.yaml b/structure_data/pdb_structures/4XNW.yaml new file mode 100644 index 00000000..ea99b94f --- /dev/null +++ b/structure_data/pdb_structures/4XNW.yaml @@ -0,0 +1,2 @@ +name: 4xnw +protein: p2ry1_human \ No newline at end of file diff --git a/structure_data/pdb_structures/4XT3.yaml b/structure_data/pdb_structures/4XT3.yaml new file mode 100644 index 00000000..dd98df20 --- /dev/null +++ b/structure_data/pdb_structures/4XT3.yaml @@ -0,0 +1,2 @@ +name: 4xt3 +protein: us28_hcmva \ No newline at end of file diff --git a/structure_data/pdb_structures/4YAY.yaml b/structure_data/pdb_structures/4YAY.yaml new file mode 100644 index 00000000..a6d089fd --- /dev/null +++ b/structure_data/pdb_structures/4YAY.yaml @@ -0,0 +1,41 @@ +# PDB data + +pdb: 4yay +publication_date: '2007-11-06' +pubmed_id: '17952055' +resolution: '3.40' + +# Structure annotations + +g_protein: None +ligand: +- {name: Carazolol, role: Inverse agonist} +endogenous_ligand: +- {name: xx, id: 2} +- {name: xx, id: 2} +representative: true +preferred_chain: A +state: Inactive + +# Structure annotations + +bulges: '' +constrictions: '' +construct: 2r4s +segments: + C-term: [340, 413] + ECL1: [97, 101] + ECL2: [171, 196] + ECL3: [299, 304] + H8: [326, 339] + ICL1: [61, 66] + ICL2: [137, 146] + ICL3: [230, 266] + N-term: [1, 30] + TM1: [31, 60] + TM2: [67, 96] + TM3: [102, 136] + TM4: [147, 170] + TM5: [197, 229] + TM6: [267, 298] + TM7: [305, 325] diff --git a/structure_data/pdb_structures/4Z34.yaml b/structure_data/pdb_structures/4Z34.yaml new file mode 100644 index 00000000..4ed9aada --- /dev/null +++ b/structure_data/pdb_structures/4Z34.yaml @@ -0,0 +1,2 @@ +name: 4z34 +protein: lpar1_human \ No newline at end of file From ea36bdaeb38085df4644c8cb7ee56a24621ffd93 Mon Sep 17 00:00:00 2001 From: Alexander Sebastian Hauser Date: Tue, 11 Aug 2015 15:18:08 +0200 Subject: [PATCH 2/2] representative structure and update on structural segments --- structure_data/pdb_structures/2I37.yaml | 43 +++++++++++++++++- structure_data/pdb_structures/2YCZ.yaml | 45 ++++++++++++++++++- structure_data/pdb_structures/4S0V.yaml | 7 ++- structure_data/pdb_structures/4XNW.yaml | 44 ++++++++++++++++++- structure_data/pdb_structures/4XT3.yaml | 47 +++++++++++++++++++- structure_data/pdb_structures/4YAY.yaml | 58 +++++++++++++------------ structure_data/pdb_structures/4Z34.yaml | 43 +++++++++++++++++- 7 files changed, 246 insertions(+), 41 deletions(-) diff --git a/structure_data/pdb_structures/2I37.yaml b/structure_data/pdb_structures/2I37.yaml index d8a61ba6..0075dc6a 100644 --- a/structure_data/pdb_structures/2I37.yaml +++ b/structure_data/pdb_structures/2I37.yaml @@ -1,2 +1,41 @@ -name: 2i37 -protein: opsd_bovin \ No newline at end of file +# PDB data + +pdb: 2i37 +publication_date: '2006-10-17' +pubmed_id: '17060607' +resolution: '4.15' + +# Structure annotations + +g_protein: None +ligand: +- {name: None, role: nan} +endogenous_ligand: +- {name: Retinal, id: 6670} +preferred_chain: A +state: Inactive + +# Structure annotations + +construct: 2i37 +segments: + C-term: [322, 348] + ECL1: [101, 105] + ECL2: [173, 199] + ECL3: [278, 289] + H8: [309, 321] + ICL1: [65, 72] + ICL2: [140, 149] + ICL3: [226, 241] + N-term: [1, 35] + TM1: [36, 64] + TM2: [73, 100] + TM3: [103, 139] + TM4: [150, 172] + TM5: [200, 225] + TM6: [242, 277] + TM7: [290, 308] +bulges: + TM2: [2x551] +constrictions: + TM7: [7x44] \ No newline at end of file diff --git a/structure_data/pdb_structures/2YCZ.yaml b/structure_data/pdb_structures/2YCZ.yaml index 9d3c1f46..5090b9bc 100644 --- a/structure_data/pdb_structures/2YCZ.yaml +++ b/structure_data/pdb_structures/2YCZ.yaml @@ -1,2 +1,43 @@ -name: 2ycz -protein: adrb1_melga \ No newline at end of file +# PDB data + +pdb: 2ycz +publication_date: '2011-06-01' +pubmed_id: '21540331' +resolution: '3.65' + +# Structure annotations + +g_protein: None +ligand: +- {name: Iodocyanopindolol, role: Antagonist} +endogenous_ligand: +- {name: noradrenaline, id: 484} +preferred_chain: B +state: Inactive +representative: true + +# Structure annotations + +construct: 2ycz +segments: + C-term: [358, 483] + ECL1: [105, 110] + ECL2: [179, 240] + ECL3: [316, 322] + H8: [347, 357] + ICL1: [69, 74] + ICL2: [145, 154] + ICL3: [237, 277] + N-term: [1, 33] + TM1: [34, 68] + TM2: [75, 104] + TM3: [111, 144] + TM4: [155, 178] + TM5: [205, 236] + TM6: [237, 315] + TM7: [323, 346] +bulges: + TM2: [2x551] + TM5: [5x461] +constrictions: + TM7: [7x44] \ No newline at end of file diff --git a/structure_data/pdb_structures/4S0V.yaml b/structure_data/pdb_structures/4S0V.yaml index 9a38c33c..ba8173cd 100644 --- a/structure_data/pdb_structures/4S0V.yaml +++ b/structure_data/pdb_structures/4S0V.yaml @@ -1,9 +1,9 @@ # PDB data -pdb: 4S0V +pdb: 4s0v publication_date: '2015-01-26' pubmed_id: '25533960' -resolution: '2.50' +resolution: '2.5' # Structure annotations @@ -15,7 +15,6 @@ endogenous_ligand: - {name: Orexin-B, id: 1699} preferred_chain: A state: Inactive -representative: true # Structure annotations @@ -41,4 +40,4 @@ bulges: TM2: [2x551] TM5: [5x461] constrictions: - TM7: [7x44] \ No newline at end of file + TM7: [7x44] diff --git a/structure_data/pdb_structures/4XNW.yaml b/structure_data/pdb_structures/4XNW.yaml index ea99b94f..fad13e8a 100644 --- a/structure_data/pdb_structures/4XNW.yaml +++ b/structure_data/pdb_structures/4XNW.yaml @@ -1,2 +1,42 @@ -name: 4xnw -protein: p2ry1_human \ No newline at end of file +# PDB data + +pdb: 4xnw +publication_date: '2015-04-01' +pubmed_id: '25822790' +resolution: '2.7' + +# Structure annotations + +g_protein: None +ligand: +- {name: MRS2500, role: nan} +endogenous_ligand: +- {name: adenosine diphosphate, id: 1712} +preferred_chain: A +state: Inactive +representative: true + +# Structure annotations + +construct: 4xnw +segments: + C-term: [327, 334] + ECL1: [113,119] + ECL2: [189, 210] + ECL3: [286, 299] + ICL1: [80, 84] + ICL2: [155, 164] + ICL3_1: [245,247] + ICL3_2: [253,254] + N-term: [36, 47] + TM1: [48, 79] + TM2: [85, 112] + TM3: [120, 154] + TM4: [165, 188] + TM5: [211, 244] + TM6: [255, 285] + TM7: [300, 326] +bulges: + TM6: [6x451] +constrictions: + TM7: [7x44] diff --git a/structure_data/pdb_structures/4XT3.yaml b/structure_data/pdb_structures/4XT3.yaml index dd98df20..bc2d816d 100644 --- a/structure_data/pdb_structures/4XT3.yaml +++ b/structure_data/pdb_structures/4XT3.yaml @@ -1,2 +1,45 @@ -name: 4xt3 -protein: us28_hcmva \ No newline at end of file +# PDB data + +pdb: 4xt3 +publication_date: '2015-03-04' +pubmed_id: '25745166' +resolution: '3.8' + +# Structure annotations + +g_protein: None +ligand: +- {name: CX3CL1, role: Agonist} +endogenous_ligand: +- {name: CX3CL1, id: 856} +preferred_chain: A +state: Inactive +representative: true + +# Structure annotations + +construct: 4xt3 +segments: + C-term: [307, 308] + ECL1_1: [95, 96] + ECL1_2: [100, 103] + ECL2: [164, 182] + ECL3: [256, 262] + H8: [295, 306] + ICL1: [61, 66] + ICL2: [135, 141] + ICL3: [216, 223] + N-term: [18, 25] + TM1: [26, 60] + TM2: [67, 94] + TM3: [104, 134] + TM4: [142, 163] + TM5: [183, 215] + TM6: [224, 255] + TM7: [263, 294] +bulges: + TM2: [2x551] + TM5: [5x461] +constrictions: + TM7: [7x44] + TM4: [4x58] \ No newline at end of file diff --git a/structure_data/pdb_structures/4YAY.yaml b/structure_data/pdb_structures/4YAY.yaml index a6d089fd..21940bd5 100644 --- a/structure_data/pdb_structures/4YAY.yaml +++ b/structure_data/pdb_structures/4YAY.yaml @@ -1,41 +1,45 @@ # PDB data pdb: 4yay -publication_date: '2007-11-06' -pubmed_id: '17952055' -resolution: '3.40' +publication_date: '2015-04-22' +pubmed_id: '25913193' +resolution: '2.9' # Structure annotations g_protein: None ligand: -- {name: Carazolol, role: Inverse agonist} -endogenous_ligand: -- {name: xx, id: 2} -- {name: xx, id: 2} -representative: true +- {name: ZD7155, role: Antagonist} +endogenous_ligand: +- {name: Angiotensin II, id: 2504} preferred_chain: A state: Inactive +representative: true # Structure annotations -bulges: '' -constrictions: '' -construct: 2r4s +construct: 4yay segments: - C-term: [340, 413] - ECL1: [97, 101] - ECL2: [171, 196] - ECL3: [299, 304] - H8: [326, 339] - ICL1: [61, 66] - ICL2: [137, 146] - ICL3: [230, 266] - N-term: [1, 30] - TM1: [31, 60] - TM2: [67, 96] - TM3: [102, 136] - TM4: [147, 170] - TM5: [197, 229] - TM6: [267, 298] - TM7: [305, 325] + C-term: [317, 317] + ECL1: [90, 97] + ECL2_1: [165, 172] + ECL2_2: [177, 185] + ECL2_3: [190, 195] + ECL3: [269, 273] + H8: [306, 316] + ICL1: [56, 61] + ICL2: [132,137] + ICL3: [221, 224] + N-term: [18, 26] + TM1: [27, 55] + TM2: [62, 89] + TM3: [98, 131] + TM4: [138, 164] + TM5: [196, 220] + TM6: [236, 268] + TM7: [274, 305] +bulges: + TM5: [5x461] +constrictions: + TM7: [7x44] + TM4: [4x57] \ No newline at end of file diff --git a/structure_data/pdb_structures/4Z34.yaml b/structure_data/pdb_structures/4Z34.yaml index 4ed9aada..e2be6755 100644 --- a/structure_data/pdb_structures/4Z34.yaml +++ b/structure_data/pdb_structures/4Z34.yaml @@ -1,2 +1,41 @@ -name: 4z34 -protein: lpar1_human \ No newline at end of file +# PDB data + +pdb: 4z34 +publication_date: '2015-06-03' +pubmed_id: '26091040' +resolution: '3.0' + +# Structure annotations + +g_protein: None +ligand: +- {name: ONO-9780307, role: Antagonist} +endogenous_ligand: +- {name: LPA, id: 2906} +preferred_chain: A +state: Inactive +representative: true + +# Structure annotations + +construct: 4z34 +segments: + C-term: [327, 327] + ECL1: [109, 117] + ECL2: [185, 203] + ECL3: [283, 293] + H8: [315, 326] + ICL1: [77, 84] + ICL2: [151, 157] + ICL3: [248, 249] + N-term: [20, 46] + TM1: [47, 76] + TM2: [85,108] + TM3: [118, 150] + TM4: [158, 184] + TM5: [204, 232] + TM6: [250, 282] + TM7: [294, 314] +bulges: '' +constrictions: + TM7: [7x44] \ No newline at end of file