MolNFT v1 · #176744 · protein
Cryo-EM structure of human V2 vasopressin receptor in complex with an gs protein
7DW9 · Vasopressin V2 receptor: “Cryo-EM structure of human V2 vasopressin receptor in complex with an gs protein”. Electron microscopy, 2 ligands (CLR, NH2), 14 pockets (best druggability 0.82). MolNFT v1 #176744 on GenesisL1: 3D…
- PDB
- 7DW9
- Type
- protein
- Length
- 1,283 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vasopressin V2 receptor; Guanine nucleotide-binding protein G(S) subunit alpha isoforms…
- UniProt
- P30518, P54311, P63212
- Ligands
- CLR, NH2
- Pockets
- 14 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Vasopressin V2 receptor | protein | 278 | 76% helix, 3% strand | P30518 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 238 | 46% helix, 18% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 7% helix, 48% strand | P54311 |
| Y | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 64% helix, 0% strand | P63212 |
| N | NANOBODY35 | protein | 126 | 5% helix, 42% strand | — |
| S | SCFV16 | protein | 233 | 5% helix, 48% strand | — |
| C | Cys-tyr-phe-gln-asn-cys-pro-arg-gly-NH2 | protein | 9 | 0% helix, 0% 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.82 | 0.85 | 60 | empty |
| 2 | 983 | 0.75 | 0.78 | 61 | empty |
| 3 | 1155 | 0.72 | 0.75 | 85 | empty |
| 4 | 186 | 0.70 | 0.88 | 23 | empty |
| 5 | 323 | 0.65 | 0.80 | 44 | empty |
Interfaces
9 interfaces between chains.
- B–Y · 2284 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1481 Ų buried · 21 hydrogen bonds · protein-protein
- R–A · 992 Ų buried · 9 hydrogen bonds · protein-protein
- R–C · 957 Ų buried · 12 hydrogen bonds · protein-protein
- A–N · 739 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7DW9 · Cryo-EM structure of human V2 vasopressin receptor in complex with an Gs protein · the same entry in another collection · chain C against C, TM-score 1.00
- P54311 · 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
- P30518 · AlphaFold monomer V2.0 prediction for vasopressin V2 receptor (P30518) · a predicted model of the same protein · chain R against A, TM-score 0.89
- P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain Y against A, TM-score 0.68
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 P30518
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7DW9 · PDBe 7DW9 · UniProt P30518 · UniProt P54311 · UniProt P63212
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