MolNFT v1 · #164004 · protein
Cryo-EM structure of rhinovirus-A89
6SK7 · VP1 capsid protein: “Cryo-EM structure of rhinovirus-A89”. Electron microscopy, 15 pockets (best druggability 0.72). MolNFT v1 #164004 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SK7
- Type
- protein
- Length
- 770 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1 capsid protein; VP2 capsid protein; VP3 capsid protein; VP4 capsid protein
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P07210, D3KZ50
- Pockets
- 15 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 capsid protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 285 | 14% helix, 29% strand | P07210 |
| B | VP2 capsid protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 254 | 13% helix, 36% strand | P07210 |
| C | VP3 capsid protein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 214 | 11% helix, 36% strand | P07210 |
| D | VP4 capsid protein | protein | 17 | 18% helix, 0% strand | D3KZ50 |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.72 | 0.98 | 19 | empty |
| 2 | 200 | 0.59 | 0.81 | 34 | empty |
| 3 | 228 | 0.54 | 0.77 | 22 | empty |
| 4 | 108 | 0.50 | 0.81 | 23 | empty |
| 5 | 136 | 0.50 | 0.79 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–C · 3210 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2041 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1627 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 382 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 234 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6SK7 · Cryo-EM structure of rhinovirus-A89 · 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 P07210
- Every structure of UniProt D3KZ50
- Elsewhere: RCSB PDB 6SK7 · PDBe 6SK7 · UniProt P07210 · UniProt D3KZ50
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