MolNFT v1 · #52320 · protein
VAMP7 longin domain hrb peptide complex
2VX8 · Nucleoporin-like protein rip, vesicle-associated membrane…: “VAMP7 longin domain hrb peptide complex”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.52). MolNFT v1 #52320 on GenesisL1: 3D structure, binding sites…
- PDB
- 2VX8
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin-like protein rip, vesicle-associated membrane protein 7
- UniProt
- P52594, P70280
- Ligands
- CL
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoporin-like protein rip, vesicle-associated membrane protein 7 | protein | 136 | 32% helix, 29% strand | P52594, P70280 |
| B | Nucleoporin-like protein rip, vesicle-associated membrane protein 7 | protein | 138 | 38% helix, 30% strand | P52594, P70280 |
| C | Nucleoporin-like protein rip, vesicle-associated membrane protein 7 | protein | 132 | 34% helix, 31% strand | P52594, P70280 |
| D | Nucleoporin-like protein rip, vesicle-associated membrane protein 7 | protein | 134 | 34% helix, 31% strand | P52594, P70280 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.52 | 0.74 | 46 | CL |
| 2 | 122 | 0.47 | 0.79 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2059 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 212 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 170 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 111 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VX8 · Vamp7 longin domain Hrb peptide complex · the same entry in another collection · chain A against A, TM-score 1.00
- P70280 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 7 (P70280) · a predicted model of the same protein · chain C against A, TM-score 0.82
- P52594 · AlphaFold monomer V2.0 prediction for arf-gap domain and fg repeat- containing protein 1… · a predicted model of the same protein · chain D against A, TM-score 0.36
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 P52594
- Every structure of UniProt P70280
- Elsewhere: RCSB PDB 2VX8 · PDBe 2VX8 · UniProt P52594 · UniProt P70280
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