Research workbench
Crystal structure of zika virus NS5 methyltransferase bound to SAM and RNA analogue (M7GPPPA)
Analyse Crystal structure of zika virus NS5 methyltransferase bound to SAM and RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZ2
- Type
- protein
- Length
- 777 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5 mtase
- UniProt
- A0A140E7U5
- Ligands
- SAM, GTA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | NS5 mtase | protein | 259 | 36% helix, 15% strand | A0A140E7U5 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.77 | 0.82 | 86 | SAM |
| 2 | 799 | 0.70 | 0.76 | 60 | empty |
| 3 | 489 | 0.66 | 0.78 | 47 | SAM |
| 4 | 277 | 0.64 | 0.81 | 33 | SAM |
| 5 | 87 | 0.48 | 0.82 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 400 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5WZ2 · Crystal structure of Zika virus NS5 methyltransferase bound to SAM and RNA analogue… · 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 5WZ2 · PDBe 5WZ2 · UniProt A0A140E7U5
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