MolNFT v1 · #114946 · protein
Crystal structure of coxsackievirus A16
5C4W · VP1: “Crystal structure of coxsackievirus A16”. X-ray diffraction, 4 ligands (SPH, K, NA), 14 pockets (best druggability 0.84). MolNFT v1 #114946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C4W
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- I3W9E1
- Ligands
- SPH, K, NA, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 287 | 11% helix, 29% strand | I3W9E1 |
| B | VP2 | protein | 245 | 14% helix, 37% strand | I3W9E1 |
| C | VP3 | protein | 242 | 13% helix, 30% strand | I3W9E1 |
| D | VP4 | protein | 58 | 12% helix, 9% strand | I3W9E1 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A, C
- NA · Sodium ion · metal · chains A, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.84 | 0.91 | 59 | SPH |
| 2 | 119 | 0.50 | 0.81 | 18 | empty |
| 3 | 152 | 0.45 | 0.75 | 24 | CL |
| 4 | 109 | 0.44 | 0.78 | 21 | empty |
| 5 | 154 | 0.44 | 0.75 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4030 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 2388 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 1664 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1610 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1107 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5C4W · Crystal structure of coxsackievirus A16 · 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 5C4W · PDBe 5C4W · UniProt I3W9E1
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