MolNFT v1 · #126437 · protein
Crystal structure of the full-length zika virus NS5 protein (human isolate Z1106033)
5M2Z: “Crystal structure of the full-length zika virus NS5 protein (human isolate Z1106033)”. X-ray diffraction, 3 ligands (SAH, ZN, PO4), 20 pockets (best druggability 0.81). MolNFT v1 #126437 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5M2Z
- Type
- protein
- Length
- 5,298 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5
- UniProt
- A0A172HA24
- Ligands
- SAH, ZN, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D, E, F | NS5 | protein | 883 | 43% helix, 14% strand | A0A172HA24 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains C, E, F
- ZN · Zinc ion · metal · 11 copies · chains A, C, B, D, E, F
- PO4 · Phosphate ion · ion · 17 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 | 1005 | 0.81 | 0.82 | 86 | PO4 |
| 2 | 986 | 0.81 | 0.82 | 92 | PO4 |
| 3 | 1037 | 0.81 | 0.82 | 89 | PO4 |
| 4 | 1036 | 0.79 | 0.81 | 113 | PO4, SAH |
| 5 | 1105 | 0.79 | 0.80 | 113 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1772 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1742 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1711 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 1045 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 891 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5M2Z · Crystal structure of the full-length Zika virus NS5 protein (Human isolate Z1106033) · 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 A0A172HA24
- Elsewhere: RCSB PDB 5M2Z · PDBe 5M2Z · UniProt A0A172HA24
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