Research workbench
Structure of zika virus NS5 RNA polymerase domain
Analyse Structure of zika virus NS5 RNA polymerase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U0C
- Type
- protein
- Length
- 4,980 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5 RNA polymerase domain
- EC
- 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- Q32ZE1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS5 RNA polymerase domain (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 624 | 44% helix, 12% strand | Q32ZE1 |
| B, C | NS5 RNA polymerase domain (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 621 | 44% helix, 11% strand | Q32ZE1 |
| D | NS5 RNA polymerase domain (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 623 | 45% helix, 11% strand | Q32ZE1 |
| E | NS5 RNA polymerase domain (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 622 | 45% helix, 11% strand | Q32ZE1 |
| F | NS5 RNA polymerase domain (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 622 | 45% helix, 11% strand | Q32ZE1 |
| G | NS5 RNA polymerase domain (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 624 | 45% helix, 11% strand | Q32ZE1 |
| H | NS5 RNA polymerase domain (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 623 | 45% helix, 11% strand | Q32ZE1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.83 | 0.85 | 100 | empty |
| 2 | 1055 | 0.83 | 0.84 | 104 | empty |
| 3 | 933 | 0.83 | 0.84 | 95 | empty |
| 4 | 598 | 0.82 | 0.87 | 85 | empty |
| 5 | 884 | 0.81 | 0.84 | 87 | empty |
Interfaces
12 interfaces between chains.
- A–G · 817 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 777 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 759 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 756 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 750 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5U0C · Structure of Zika virus NS5 RNA polymerase domain · 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 Q32ZE1
- Elsewhere: RCSB PDB 5U0C · PDBe 5U0C · UniProt Q32ZE1
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