Research workbench
Crystal structure of 2C helicase from enterovirus 71 (EV71)
Analyse Crystal structure of 2C helicase from enterovirus 71 (EV71) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GQ1
- Type
- protein
- Length
- 1,157 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- Ligands
- ZN, PO4
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 207 | 31% helix, 19% strand | — |
| B | Genome polyprotein | protein | 198 | 33% helix, 18% strand | — |
| C | Genome polyprotein | protein | 197 | 30% helix, 20% strand | — |
| D | Genome polyprotein | protein | 197 | 31% helix, 20% strand | — |
| E | Genome polyprotein | protein | 185 | 32% helix, 22% strand | — |
| F | Genome polyprotein | protein | 173 | 31% helix, 18% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.72 | 0.78 | 58 | empty |
| 2 | 764 | 0.69 | 0.76 | 52 | empty |
| 3 | 532 | 0.68 | 0.78 | 70 | PO4 |
| 4 | 321 | 0.67 | 0.82 | 43 | empty |
| 5 | 302 | 0.53 | 0.75 | 31 | empty |
Interfaces
10 interfaces between chains.
- A–D · 734 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 601 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 600 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 282 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 271 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5GQ1 · Crystal structure of 2C helicase from enterovirus 71 (EV71) · 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
- Elsewhere: RCSB PDB 5GQ1 · PDBe 5GQ1
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