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Room temperature structure of SARS-cov-2 NSP10/NSP16 methyltransferase in a complex with SAM determined by fixed-target serial crystallography
Analyse Room temperature structure of SARS-cov-2 NSP10/NSP16 methyltransferase in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XKM
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-O-methyltransferase; Non-structural protein 10
- EC
- 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- SAM, ZN, CL
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 298 | 30% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 115 | 24% helix, 15% strand | P0DTD1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.51 | 0.75 | 44 | CL, SAM |
| 2 | 121 | 0.45 | 0.77 | 18 | empty |
| 3 | 55 | 0.34 | 0.78 | 15 | empty |
| 4 | 75 | 0.30 | 0.74 | 18 | empty |
| 5 | 53 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 944 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XKM · Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransferase in a Complex with… · 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 P0DTD1
- Elsewhere: RCSB PDB 6XKM · PDBe 6XKM · UniProt P0DTD1
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