Research workbench
Crystal structure of human enterovirus 71 in complex with the uncoating inhibitor GPP4
Analyse Crystal structure of human enterovirus 71 in complex with the uncoating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CDW
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- B2ZUN0
- Ligands
- VR2, NA
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 297 | 14% helix, 27% strand | B2ZUN0 |
| B | VP2 | protein | 245 | 14% helix, 38% strand | B2ZUN0 |
| C | VP3 | protein | 242 | 13% helix, 30% strand | B2ZUN0 |
| D | VP4 | protein | 58 | 12% helix, 12% strand | B2ZUN0 |
Ligands and binding sites
- VR2 · 1-[(3S)-5-(4-iodanylphenoxy)-3-methyl-pentyl]-3-pyridin-4-yl-imidazolidin-2-one · ligand · chains A, C
- NA · Sodium ion · metal · 2 copies · chains C, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.80 | 0.87 | 60 | VR2 |
| 2 | 278 | 0.60 | 0.79 | 44 | empty |
| 3 | 80 | 0.50 | 0.84 | 18 | empty |
| 4 | 192 | 0.49 | 0.76 | 28 | empty |
| 5 | 126 | 0.48 | 0.79 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4034 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2706 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1659 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1511 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1145 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4CDW · Crystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP4 · 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 B2ZUN0
- Elsewhere: RCSB PDB 4CDW · PDBe 4CDW · UniProt B2ZUN0
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