MolNFT v1 · #115060 · protein
Crystal structure of recombinant coxsackievirus A16 capsid
5C8C · VP1: “Crystal structure of recombinant coxsackievirus A16 capsid”. X-ray diffraction, 3 ligands (STE, K, CL), 13 pockets (best druggability 0.82). MolNFT v1 #115060 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C8C
- Type
- protein
- Length
- 787 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP0; VP3
- UniProt
- I3W9E1
- Ligands
- STE, K, CL
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 259 | 14% helix, 30% strand | I3W9E1 |
| B | VP0 | protein | 286 | 14% helix, 34% strand | I3W9E1 |
| C | VP3 | protein | 242 | 13% helix, 31% strand | I3W9E1 |
Ligands and binding sites
- STE · Stearic acid · ligand · chains A, C
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.82 | 0.91 | 50 | STE |
| 2 | 408 | 0.59 | 0.76 | 45 | empty |
| 3 | 72 | 0.57 | 0.88 | 26 | empty |
| 4 | 213 | 0.51 | 0.76 | 36 | empty |
| 5 | 168 | 0.48 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3709 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 2673 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 2457 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5C8C · Crystal structure of recombinant coxsackievirus A16 capsid · 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 I3W9E1
- Elsewhere: RCSB PDB 5C8C · PDBe 5C8C · UniProt I3W9E1
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