MolNFT v1 · #54759 · protein
Crystal structure of the NSP16 NSP10 SARS coronavirus complex
2XYV · Putative 2'-O-methyl transferase: “Crystal structure of the NSP16 NSP10 SARS coronavirus complex”. X-ray diffraction, 5 ligands (SAH, NA, ZN), 4 pockets (best druggability 0.50). MolNFT v1 #54759 on GenesisL1: 3D structure, binding…
- PDB
- 2XYV
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 2'-O-methyl transferase; Non-structural protein 10
- EC
- 2.1.1.-
- UniProt
- P0C6X7
- Ligands
- SAH, NA, ZN, MG, CL
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 2'-O-methyl transferase (EC 2.1.1.-) | protein | 285 | 30% helix, 22% strand | P0C6X7 |
| B | Non-structural protein 10 | protein | 115 | 29% helix, 13% strand | P0C6X7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.50 | 0.75 | 43 | SAH |
| 2 | 64 | 0.36 | 0.78 | 17 | empty |
| 3 | 85 | 0.35 | 0.74 | 16 | empty |
| 4 | 50 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 935 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2XYV · Crystal structure of the nsp16 nsp10 SARS coronavirus complex · 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 P0C6X7
- Elsewhere: RCSB PDB 2XYV · PDBe 2XYV · UniProt P0C6X7
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