MolNFT v2 · #183332 · protein
Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1
7JIB · 2'-O-methyltransferase: “Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of…”. X-ray diffraction at 2.65, 5 ligands (GTA, V9G, MGP), 6 pockets (best druggability 0.50). MolNFT v2…
- PDB
- 7JIB
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 2'-O-methyltransferase; Non-structural protein 10
- EC
- 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- GTA, V9G, MGP, ZN, CL
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · resolution 2.65 · 2 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 301 | 29% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 114 | 25% helix, 13% strand | P0DTD1 |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · 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 · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.50 | 0.79 | 20 | empty |
| 2 | 213 | 0.49 | 0.75 | 28 | CL, GTA, V9G |
| 3 | 62 | 0.39 | 0.80 | 15 | empty |
| 4 | 65 | 0.31 | 0.75 | 20 | empty |
| 5 | 57 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 958 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7JIB · Room temperature crystal structure of NSP10/NSP16 from SARS-cov-2 with substrates and… · 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 7JIB · PDBe 7JIB · UniProt P0DTD1
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