MolNFT v1 · #164003 · protein
Cryo-EM structure of rhinovirus-B5
6SK6 · Rhinovirus B5 VP4: “Cryo-EM structure of rhinovirus-B5”. Electron microscopy, 9 pockets (best druggability 0.79). MolNFT v1 #164003 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SK6
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhinovirus B5 VP4; Rhinovirus B5 VP2; Rhinovirus B5 VP1; Rhinovirus B5 VP3
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q80SQ3, B9V433, Q7T659
- Pockets
- 9 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Rhinovirus B5 VP4 | protein | 40 | 18% helix, 3% strand | Q80SQ3 |
| B | Rhinovirus B5 VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 252 | 12% helix, 38% strand | B9V433 |
| A | Rhinovirus B5 VP1 | protein | 273 | 11% helix, 33% strand | Q7T659 |
| C | Rhinovirus B5 VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 231 | 10% helix, 31% strand | B9V433 |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.79 | 0.88 | 62 | empty |
| 2 | 108 | 0.50 | 0.81 | 20 | empty |
| 3 | 103 | 0.48 | 0.80 | 24 | empty |
| 4 | 152 | 0.48 | 0.78 | 29 | empty |
| 5 | 119 | 0.47 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3779 Ų buried · 65 hydrogen bonds · protein-protein
- B–A · 2077 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1550 Ų buried · 21 hydrogen bonds · protein-protein
- D–C · 845 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 828 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6SK6 · Cryo-EM structure of rhinovirus-B5 · the same entry in another collection · chain D against D, 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 Q80SQ3
- Every structure of UniProt B9V433
- Every structure of UniProt Q7T659
- Elsewhere: RCSB PDB 6SK6 · PDBe 6SK6 · UniProt Q80SQ3 · UniProt B9V433 · UniProt Q7T659
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