Research workbench
Crystal structure of zika virus NS5 methyltransferase bound to S- adenosyl-L-methionine
Analyse Crystal structure of zika virus NS5 methyltransferase bound to S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZ1
- Type
- protein
- Length
- 2,072 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5 methyltransferase
- UniProt
- A0A140E7U5
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | NS5 methyltransferase | protein | 259 | 35% helix, 15% strand | A0A140E7U5 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 8 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.79 | 0.81 | 109 | SAM |
| 2 | 1065 | 0.77 | 0.79 | 77 | empty |
| 3 | 911 | 0.75 | 0.78 | 82 | SAM |
| 4 | 1043 | 0.74 | 0.77 | 114 | SAM |
| 5 | 536 | 0.66 | 0.77 | 49 | SAM |
Interfaces
19 interfaces between chains.
- D–G · 540 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 531 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 376 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 357 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5WZ1 · Crystal structure of Zika virus NS5 methyltransferase bound to S-adenosyl-L-methionine · 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 A0A140E7U5
- Elsewhere: RCSB PDB 5WZ1 · PDBe 5WZ1 · UniProt A0A140E7U5
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