Merged in AlexHauser/gpcrdb_data-alex (pull request protwis#1)

pdb-structures
pszgaspar · Aug 18, 2015 · 5b79b21 · 5b79b21
2 parents 2cbce3b + ea36bda
commit 5b79b21
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diff --git a/structure_data/constructs/2I37.yaml b/structure_data/constructs/2I37.yaml
@@ -0,0 +1,2 @@
+name: 2i37
+protein: opsd_bovin
diff --git a/structure_data/constructs/2YCZ.yaml b/structure_data/constructs/2YCZ.yaml
@@ -0,0 +1,2 @@
+name: 2ycz
+protein: adrb1_melga
diff --git a/structure_data/constructs/4XNW.yaml b/structure_data/constructs/4XNW.yaml
@@ -0,0 +1,2 @@
+name: 4xnw
+protein: p2ry1_human
diff --git a/structure_data/constructs/4XT3.yaml b/structure_data/constructs/4XT3.yaml
@@ -0,0 +1,2 @@
+name: 4xt3
+protein: us28_hcmva
diff --git a/structure_data/constructs/4YAY.yaml b/structure_data/constructs/4YAY.yaml
@@ -0,0 +1,2 @@
+name: 4yay
+protein: agtr1_human
diff --git a/structure_data/constructs/4Z34.yaml b/structure_data/constructs/4Z34.yaml
@@ -0,0 +1,2 @@
+name: 4z34
+protein: lpar1_human
diff --git a/structure_data/pdb_structures/2I37.yaml b/structure_data/pdb_structures/2I37.yaml
@@ -0,0 +1,41 @@
+# 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]
diff --git 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
@@ -0,0 +1,43 @@
+# 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]
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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