Research workbench
Cryo-EM structure of human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and gs
Analyse Cryo-EM structure of human vasoactive intestinal polypeptide receptor 2 (VIP2R)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VQX
- Type
- protein
- Length
- 1,148 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- UniProt
- P04896, P54311, P63212, P18509, P41587
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 237 | 44% helix, 18% strand | P04896 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 47% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 53% helix, 0% strand | P63212 |
| L | Pituitary adenylate cyclase-activating polypeptide 27 | protein | 27 | 93% helix, 0% strand | P18509 |
| N | Nanobody-35 | protein | 128 | 2% helix, 45% strand | — |
| R | Vasoactive intestinal polypeptide receptor 2 | protein | 361 | 68% helix, 3% strand | P41587 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.83 | 0.85 | 74 | empty |
| 2 | 932 | 0.76 | 0.79 | 61 | empty |
| 3 | 590 | 0.74 | 0.81 | 78 | empty |
| 4 | 962 | 0.70 | 0.75 | 58 | empty |
| 5 | 157 | 0.55 | 0.81 | 21 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2081 Ų buried · 14 hydrogen bonds · protein-protein
- L–R · 1787 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1484 Ų buried · 26 hydrogen bonds · protein-protein
- A–R · 1020 Ų buried · 12 hydrogen bonds · protein-protein
- A–N · 882 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7VQX · Cryo-EM structure of human vasoactive intestinal polypeptide receptor 2 (VIP2R) in… · the same entry in another collection · chain R against R, 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
- P41587 · AlphaFold monomer V2.0 prediction for vasoactive intestinal polypeptide receptor 2… · a predicted model of the same protein · chain R against A, TM-score 0.90
- P04896 · 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 0.84
- 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 0.83
- 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 G 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 P04896
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Every structure of UniProt P18509
- Every structure of UniProt P41587
- Elsewhere: RCSB PDB 7VQX · PDBe 7VQX · UniProt P04896 · UniProt P54311 · UniProt P63212 · UniProt P18509 · UniProt P41587
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