Research workbench
Crystal structure of 2C helicase from enterovirus 71 (EV71) bound with atpgammas
Analyse Crystal structure of 2C helicase from enterovirus 71 (EV71) bound with atpgammas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GRB
- Type
- protein
- Length
- 1,241 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EV71 2C ATPase
- Ligands
- AGS, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EV71 2C ATPase | protein | 211 | 31% helix, 17% strand | — |
| B | EV71 2C ATPase | protein | 212 | 30% helix, 17% strand | — |
| C | EV71 2C ATPase | protein | 199 | 33% helix, 19% strand | — |
| D | EV71 2C ATPase | protein | 203 | 31% helix, 19% strand | — |
| E, F | EV71 2C ATPase | protein | 208 | 25% helix, 17% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
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 | 1096 | 0.81 | 0.82 | 95 | empty |
| 2 | 1024 | 0.72 | 0.76 | 76 | AGS |
| 3 | 1026 | 0.70 | 0.75 | 73 | empty |
| 4 | 181 | 0.53 | 0.79 | 25 | empty |
| 5 | 117 | 0.52 | 0.82 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–C · 701 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 659 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 592 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 568 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 462 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5GRB · Crystal structure of 2C helicase from enterovirus 71 (EV71) bound with ATPgammaS · 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 5GRB · PDBe 5GRB
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.