MolNFT v1 · #111610 · protein
Crystal structure of an enterovirus 71/COXSACKIEVIRUS A16 chimeric virus-like particle
4YVW · Capsid protein VP1: “Crystal structure of an enterovirus 71/COXSACKIEVIRUS A16 chimeric virus-like particle”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #111610 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YVW
- Type
- protein
- Length
- 3,420 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP3; Capsid protein VP0
- UniProt
- F6KTB0
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, D, J, M | Capsid protein VP1 | protein | 225 | 8% helix, 30% strand | F6KTB0 |
| F, B, H, K, N | Capsid protein VP3 | protein | 224 | 11% helix, 35% strand | F6KTB0 |
| G, C, I, L, O | Capsid protein VP0 | protein | 235 | 10% helix, 25% strand | F6KTB0 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.84 | 0.85 | 117 | empty |
| 2 | 904 | 0.82 | 0.84 | 102 | empty |
| 3 | 984 | 0.81 | 0.83 | 118 | empty |
| 4 | 1095 | 0.81 | 0.82 | 115 | empty |
| 5 | 1186 | 0.80 | 0.82 | 109 | empty |
Interfaces
55 interfaces between chains.
- D–H · 2978 Ų buried · 45 hydrogen bonds · protein-protein
- M–N · 2970 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2928 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2927 Ų buried · 36 hydrogen bonds · protein-protein
- J–K · 2910 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4YVW · crystal structure of an enterovirus 71/coxsackievirus A16 chimeric virus-like particle · the same entry in another collection · chain E against E, 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 F6KTB0
- Elsewhere: RCSB PDB 4YVW · PDBe 4YVW · UniProt F6KTB0
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