MolNFT v2 · #215945 · protein
SARS-CoV-2 nsp10-16 methyltransferase in complex with 5-Iodotubercidin
8OV3 · 2'-O-methyltransferase nsp16: “SARS-CoV-2 nsp10-16 methyltransferase in complex with 5-Iodotubercidin”. X-ray diffraction at 1.82, 2 ligands (5ID, ZN), 4 pockets (best druggability 0.51). MolNFT v2 #215945 on GenesisL1: 3D…
- PDB
- 8OV3
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 2'-O-methyltransferase nsp16; Non-structural protein 10
- EC
- 2.1.1.57
- UniProt
- P0DTD1
- Ligands
- 5ID, ZN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · resolution 1.82 · 2 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase nsp16 (EC 2.1.1.57) | protein | 300 | 29% helix, 21% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 115 | 24% helix, 13% strand | P0DTD1 |
Ligands and binding sites
- 5ID · (2R,3R,4S,5R)-2-(4-amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)tetrahydrofuran-3, 4-diol · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.51 | 0.76 | 46 | EDO, 5ID |
| 2 | 119 | 0.45 | 0.77 | 18 | EDO |
| 3 | 61 | 0.36 | 0.78 | 16 | empty |
| 4 | 53 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 9 hydrogen bonds · protein-protein
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 8OV3 · PDBe 8OV3 · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.