Research workbench
Cryo-EM structure of an activated VIP1 receptor-G protein complex
Analyse Cryo-EM structure of an activated VIP1 receptor-G protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VN7
- Type
- protein
- Length
- 1,052 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vasoactive intestinal polypeptide receptor 1; Pituitary adenylate cyclase-activating…
- UniProt
- P18509, P63092, P62873, P59768
- Ligands
- CLR, PLM
- Pockets
- 14 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Vasoactive intestinal polypeptide receptor 1 | protein | 263 | 82% helix, 0% strand | — |
| L | Pituitary adenylate cyclase-activating polypeptide | protein | 27 | 93% helix, 0% strand | P18509 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 239 | 47% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 6% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 53% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 128 | 7% helix, 46% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.84 | 0.87 | 75 | empty |
| 2 | 1121 | 0.76 | 0.78 | 98 | empty |
| 3 | 924 | 0.75 | 0.78 | 71 | empty |
| 4 | 407 | 0.72 | 0.83 | 67 | empty |
| 5 | 58 | 0.67 | 0.96 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2189 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1530 Ų buried · 17 hydrogen bonds · protein-protein
- R–L · 1089 Ų buried · 8 hydrogen bonds · protein-protein
- A–N · 1070 Ų buried · 7 hydrogen bonds · protein-protein
- R–A · 992 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6VN7 · Cryo-EM structure of an activated VIP1 receptor-G protein complex · the same entry in another collection · chain N against N, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.93
- P18509 · AlphaFold monomer V2.0 prediction for pituitary adenylate cyclase- activating polypeptide… · a predicted model of the same protein · chain L against A, TM-score 0.86
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.83
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P18509
- Every structure of UniProt P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6VN7 · PDBe 6VN7 · UniProt P18509 · UniProt P63092 · UniProt P62873 · UniProt P59768
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