MolNFT v1 · #190026 · protein
Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and gs
7WBJ: “Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor 2 (VIP2R) in…”. Electron microscopy, 15 pockets (best druggability 0.80). MolNFT v1 #190026 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7WBJ
- Type
- protein
- Length
- 1,146 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vasoactive intestinal polypeptide receptor 2; Pituitary adenylate cyclase-activating…
- UniProt
- P41587, P18509, P04896, P54311, P63212
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Vasoactive intestinal polypeptide receptor 2 | protein | 359 | 59% helix, 4% strand | P41587 |
| L | Pituitary adenylate cyclase-activating polypeptide 27 | protein | 27 | 93% helix, 0% strand | P18509 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 237 | 45% helix, 16% strand | P04896 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 7% helix, 34% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 49% helix, 0% strand | P63212 |
| N | Nanobody-35 | protein | 128 | 0% helix, 38% strand | — |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.80 | 0.85 | 52 | empty |
| 2 | 804 | 0.73 | 0.78 | 58 | empty |
| 3 | 1172 | 0.71 | 0.75 | 87 | empty |
| 4 | 349 | 0.69 | 0.82 | 48 | empty |
| 5 | 165 | 0.65 | 0.86 | 26 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2021 Ų buried · 12 hydrogen bonds · protein-protein
- R–L · 1526 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1420 Ų buried · 14 hydrogen bonds · protein-protein
- R–A · 985 Ų buried · 12 hydrogen bonds · protein-protein
- A–N · 935 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7WBJ · Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor… · the same entry in another collection · chain N against N, 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 0.98
- 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 0.89
- 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 0.83
- 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 0.79
- 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 0.60
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 P41587
- Every structure of UniProt P18509
- Every structure of UniProt P04896
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7WBJ · PDBe 7WBJ · UniProt P41587 · UniProt P18509 · UniProt P04896 · UniProt P54311 · UniProt P63212
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