Research workbench
Crystal structure of the full-length zika virus NS5 protein (human isolate Z1106033)
Analyse Crystal structure of the full-length zika virus NS5 protein (human isolate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M2X
- Type
- protein
- Length
- 5,297 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5
- UniProt
- A0A1B2ZC85
- Ligands
- SAH, ZN, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | NS5 | protein | 883 | 43% helix, 14% strand | A0A1B2ZC85 |
| B | NS5 | protein | 882 | 43% helix, 14% strand | A0A1B2ZC85 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 11 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, D, E, F
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 | 1024 | 0.81 | 0.82 | 83 | PO4 |
| 2 | 1001 | 0.81 | 0.82 | 86 | empty |
| 3 | 1189 | 0.78 | 0.80 | 79 | empty |
| 4 | 1161 | 0.78 | 0.80 | 82 | PO4 |
| 5 | 1036 | 0.78 | 0.80 | 68 | PO4 |
Interfaces
8 interfaces between chains.
- C–D · 1754 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1721 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1652 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1158 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1152 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5M2X · Crystal structure of the full-length Zika virus NS5 protein (Human isolate Z1106033) · the same entry in another collection · chain C against C, 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 A0A1B2ZC85
- Elsewhere: RCSB PDB 5M2X · PDBe 5M2X · UniProt A0A1B2ZC85
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.