MolNFT v1 · #163913 · protein
Structure of a marine algae virus of the order picornavirales
6SHL · VP1: “Structure of a marine algae virus of the order picornavirales”. Electron microscopy, 11 pockets (best druggability 0.72). MolNFT v1 #163913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SHL
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- A0A0B6VJB4, A0A0B6VMZ2
- Pockets
- 11 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 6% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 267 | 10% helix, 28% strand | A0A0B6VJB4 |
| B | VP2 | protein | 231 | 3% helix, 29% strand | A0A0B6VJB4 |
| C | VP3 | protein | 261 | 5% helix, 34% strand | A0A0B6VJB4 |
| D | VP4 | protein | 51 | 6% helix, 2% strand | A0A0B6VMZ2 |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.72 | 0.96 | 23 | empty |
| 2 | 295 | 0.71 | 0.85 | 38 | empty |
| 3 | 68 | 0.67 | 0.94 | 21 | empty |
| 4 | 51 | 0.58 | 0.92 | 18 | empty |
| 5 | 174 | 0.56 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4367 Ų buried · 62 hydrogen bonds · protein-protein
- B–C · 1249 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1044 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 737 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 696 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6SHL · Structure of a marine algae virus of the order Picornavirales · 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 A0A0B6VJB4
- Every structure of UniProt A0A0B6VMZ2
- Elsewhere: RCSB PDB 6SHL · PDBe 6SHL · UniProt A0A0B6VJB4 · UniProt A0A0B6VMZ2
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