MolNFT v1 · #178644 · protein
Room temperature structure of SARS-cov-2 NSP10/NSP16 methyltransferase in a complex with 2'-O-methylated M7GPPPA cap-1 and sah determined by fixed-target serial crystallography
7JHE · 2'-O-methyltransferase: “Room temperature structure of SARS-cov-2 NSP10/NSP16 methyltransferase in a complex with 2'-O-methylated…”. X-ray diffraction, 5 ligands (SAH, V9G, MGP), 6 pockets (best druggability 0.54). MolNFT v1 #178644…
- PDB
- 7JHE
- Type
- protein
- Length
- 414 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
- SAH, V9G, MGP, ZN, CL
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 299 | 27% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 115 | 27% helix, 17% strand | P0DTD1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- V9G · 7-methyl-guanosine-5'-triphosphate-5'-(2'-O-methyl)-adenosine · ligand · chains A
- MGP · 7-methyl-guanosine-5'-triphosphate · 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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.54 | 0.76 | 46 | SAH, V9G |
| 2 | 123 | 0.44 | 0.77 | 20 | empty |
| 3 | 65 | 0.35 | 0.77 | 15 | empty |
| 4 | 58 | 0.33 | 0.77 | 16 | empty |
| 5 | 54 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7JHE · 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 7JHE · PDBe 7JHE · UniProt P0DTD1
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