Research workbench
Avp-V2R-galphas-BETA1-GAMMA2-NB35(T state)
Analyse Avp-V2R-galphas-BETA1-GAMMA2-NB35(T state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BB7
- Type
- protein
- Length
- 1,022 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vasopressin V2 receptor; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit…
- UniProt
- P30518, P62873, P63092, P59768
- Ligands
- NH2
- Pockets
- 16 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 33% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vasopressin V2 receptor | protein | 268 | 69% helix, 2% strand | P30518 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 9% helix, 23% strand | P62873 |
| E | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 218 | 40% helix, 3% strand | P63092 |
| F | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 60 | 47% helix, 0% strand | P59768 |
| G | Nanobody 35 | protein | 128 | 2% helix, 13% strand | — |
| H | Vasopressin | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.82 | 0.93 | 54 | empty |
| 2 | 907 | 0.81 | 0.83 | 92 | empty |
| 3 | 728 | 0.77 | 0.82 | 83 | empty |
| 4 | 657 | 0.77 | 0.82 | 71 | empty |
| 5 | 86 | 0.76 | 0.99 | 23 | empty |
Interfaces
9 interfaces between chains.
- C–F · 2251 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1519 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1273 Ų buried · 12 hydrogen bonds · protein-protein
- E–G · 1068 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 655 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7BB7 · AVP-V2R-Galphas-beta1-gamma2-Nb35(T state) · the same entry in another collection · chain H against H, 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 C against A, TM-score 0.95
- P30518 · AlphaFold monomer V2.0 prediction for vasopressin V2 receptor (P30518) · a predicted model of the same protein · chain A against A, TM-score 0.79
- 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 F against A, TM-score 0.70
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 P62873
- Every structure of UniProt P63092
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7BB7 · PDBe 7BB7 · UniProt P30518 · UniProt P62873 · UniProt P63092 · UniProt P59768
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