MolNFT v1 · #158763 · protein
Crystal structure for rva-VP3
6O3V · Protein VP3: “Crystal structure for rva-VP3”. X-ray diffraction, 2 ligands (5GP, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #158763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O3V
- Type
- protein
- Length
- 2,489 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein VP3
- UniProt
- Q1WK45
- Ligands
- 5GP, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein VP3 | protein | 828 | 36% helix, 21% strand | Q1WK45 |
| B | Protein VP3 | protein | 831 | 36% helix, 19% strand | Q1WK45 |
| C | Protein VP3 | protein | 830 | 35% helix, 22% strand | Q1WK45 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.84 | 0.85 | 102 | SO4 |
| 2 | 976 | 0.82 | 0.84 | 96 | empty |
| 3 | 1067 | 0.77 | 0.79 | 103 | SO4 |
| 4 | 160 | 0.73 | 0.91 | 25 | empty |
| 5 | 69 | 0.72 | 0.97 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 2923 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 990 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6O3V · Crystal structure for RVA-VP3 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q1WK45
- Elsewhere: RCSB PDB 6O3V · PDBe 6O3V · UniProt Q1WK45
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