Research workbench
Structure of coxsackievirus A16 in complex with GPP3
Analyse Structure of coxsackievirus A16 in complex with GPP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ABJ
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- I3W9E1
- Ligands
- YM2, NA, CL
- Pockets
- 13 · 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 | 286 | 13% helix, 28% strand | I3W9E1 |
| B | VP2 | protein | 245 | 14% helix, 37% strand | I3W9E1 |
| C | VP3 | protein | 242 | 12% helix, 30% strand | I3W9E1 |
| D | VP4 | protein | 51 | 14% helix, 10% strand | I3W9E1 |
Ligands and binding sites
- YM2 · 1-[(3S)-5-[4-[(E)-ethoxyiminomethyl]phenoxy]-3-methyl-pentyl]-3-pyridin-4-yl-imidazolidin-2-one · ligand · chains A, C
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.84 | 0.91 | 65 | YM2 |
| 2 | 220 | 0.58 | 0.80 | 38 | empty |
| 3 | 155 | 0.54 | 0.80 | 27 | empty |
| 4 | 171 | 0.46 | 0.76 | 38 | empty |
| 5 | 163 | 0.46 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4035 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 2324 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1681 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1504 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1012 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5ABJ · Structure of Coxsackievirus A16 in complex with GPP3 · 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 5ABJ · PDBe 5ABJ · UniProt I3W9E1
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