Research workbench
Rotavirus a-VP3 (rva-VP3)
Analyse Rotavirus a-VP3 (rva-VP3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O6B
- Type
- protein
- Length
- 3,312 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein VP3
- EC
- 3.1.4.-, 2.7.7.50, 2.1.1.56
- UniProt
- Q1WK45
- Ligands
- 5GP
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein VP3 (EC 3.1.4.-, 2.7.7.50, 2.1.1.56) | protein | 828 | 32% helix, 20% strand | Q1WK45 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
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 | 821 | 0.82 | 0.85 | 73 | empty |
| 2 | 799 | 0.82 | 0.85 | 70 | empty |
| 3 | 958 | 0.80 | 0.82 | 93 | empty |
| 4 | 1033 | 0.80 | 0.81 | 98 | empty |
| 5 | 1050 | 0.76 | 0.78 | 89 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2913 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2901 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1098 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 1079 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 773 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6O6B · Rotavirus A-VP3 (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 6O6B · PDBe 6O6B · UniProt Q1WK45
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