Research workbench
Crystal structure of the NSP16 NSP10 SARS coronavirus complex
Analyse Crystal structure of the NSP16 NSP10 SARS coronavirus complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XYQ
- Type
- protein
- Length
- 409 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
- 6 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 2'-O-methyl transferase (EC 2.1.1.-) | protein | 287 | 29% helix, 21% strand | P0C6X7 |
| B | Non-structural protein 10 | protein | 122 | 27% helix, 12% strand | P0C6X7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.48 | 0.75 | 34 | SAH |
| 2 | 112 | 0.45 | 0.78 | 18 | empty |
| 3 | 61 | 0.33 | 0.77 | 15 | empty |
| 4 | 82 | 0.32 | 0.73 | 24 | empty |
| 5 | 60 | 0.30 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2XYQ · 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 2XYQ · PDBe 2XYQ · UniProt P0C6X7
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