Research workbench
Avp-V2R-galphas-BETA1-GAMMA2-NB35 (L state)
Analyse Avp-V2R-galphas-BETA1-GAMMA2-NB35 (L state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BB6
- Type
- protein
- Length
- 1,017 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
- 17 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vasopressin V2 receptor | protein | 270 | 66% helix, 3% strand | P30518 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 32% strand | P62873 |
| E | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 214 | 47% helix, 4% strand | P63092 |
| F | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 49% helix, 0% strand | P59768 |
| H | Arginine-vasopressin | protein | 9 | 0% helix, 0% strand | — |
| B | Nanobody 35 | protein | 128 | 5% helix, 39% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.83 | 0.85 | 80 | empty |
| 2 | 949 | 0.82 | 0.84 | 88 | empty |
| 3 | 509 | 0.82 | 0.88 | 55 | empty |
| 4 | 215 | 0.81 | 0.94 | 42 | empty |
| 5 | 487 | 0.74 | 0.83 | 54 | empty |
Interfaces
7 interfaces between chains.
- C–F · 2197 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1453 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1153 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 798 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 608 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7BB6 · AVP-V2R-Galphas-beta1-gamma2-Nb35 (L state) · the same entry in another collection · chain B against B, 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 0.97
- P30518 · AlphaFold monomer V2.0 prediction for vasopressin V2 receptor (P30518) · a predicted model of the same protein · chain A against A, TM-score 0.81
- 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 0.81
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 7BB6 · PDBe 7BB6 · UniProt P30518 · UniProt P62873 · UniProt P63092 · UniProt P59768
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