MolNFT v1 · #54755 · protein
Crystal structure of the NSP16 NSP10 SARS coronavirus complex
2XYR · Putative 2'-O-methyl transferase: “Crystal structure of the NSP16 NSP10 SARS coronavirus complex”. X-ray diffraction, 5 ligands (SFG, ZN, NA), 5 pockets (best druggability 0.56). MolNFT v1 #54755 on GenesisL1: 3D structure, binding…
- PDB
- 2XYR
- Type
- protein
- Length
- 402 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
- SFG, ZN, NA, MG, CL
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 2'-O-methyl transferase (EC 2.1.1.-) | protein | 286 | 28% helix, 22% strand | P0C6X7 |
| B | Non-structural protein 10 | protein | 116 | 29% helix, 13% strand | P0C6X7 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- NA · Sodium ion · metal · chains A
- 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.56 | 0.76 | 44 | SFG |
| 2 | 103 | 0.42 | 0.77 | 18 | empty |
| 3 | 58 | 0.34 | 0.77 | 12 | empty |
| 4 | 71 | 0.30 | 0.74 | 22 | CL |
| 5 | 52 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 937 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2XYR · 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 2XYR · PDBe 2XYR · UniProt P0C6X7
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