MolNFT v1 · #120156 · protein
Crystal structure of 2C helicase from enterovirus 71 (EV71) bound with atpgammas
5GRB · EV71 2C ATPase: “Crystal structure of 2C helicase from enterovirus 71 (EV71) bound with atpgammas”. X-ray diffraction, 2 ligands (AGS, ZN), 11 pockets (best druggability 0.81). MolNFT v1 #120156 on GenesisL1: 3D structure, binding…
- 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
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