MolNFT v1 · #180071 · protein
Room temperature structure of SARS-cov-2 NSP10/16 methyltransferase in a complex with cap-0 and SAM determined by pink-beam serial crystallography
7KOA · 2'-O-methyltransferase: “Room temperature structure of SARS-cov-2 NSP10/16 methyltransferase in a complex with cap-0 and SAM…”. X-ray diffraction, 3 ligands (GTA, SAM, ZN), 5 pockets (best druggability 0.54). MolNFT v1 #180071 on…
- PDB
- 7KOA
- Type
- protein
- Length
- 419 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
- GTA, SAM, ZN
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 297 | 27% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 122 | 23% helix, 14% strand | P0DTD1 |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · 2 copies · chains A
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains 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 | 287 | 0.54 | 0.75 | 48 | GTA, SAM |
| 2 | 77 | 0.39 | 0.78 | 18 | empty |
| 3 | 67 | 0.35 | 0.77 | 18 | empty |
| 4 | 65 | 0.34 | 0.77 | 15 | empty |
| 5 | 51 | 0.24 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7KOA · Room Temperature Structure of SARS-CoV-2 Nsp10/16 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 7KOA · PDBe 7KOA · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.