MolNFT v2 · #227964 · protein
SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA (Cap0-analog)/m7GpppAm (Cap1-analog)
9EMV · 2'-O-methyltransferase nsp16: “SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA (Cap0-analog)/m7GpppAm…”. X-ray diffraction at 2.34, 5 ligands (SGV, GTA, SAH), 5 pockets (best druggability 0.55). MolNFT…
- PDB
- 9EMV
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.34
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 2'-O-methyltransferase nsp16; Non-structural protein 10
- EC
- 2.1.1.57
- UniProt
- P0DTD1
- Ligands
- SGV, GTA, SAH, V9G, ZN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · resolution 2.34 · 2 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase nsp16 (EC 2.1.1.57) | protein | 300 | 28% helix, 23% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 115 | 23% helix, 15% strand | P0DTD1 |
Ligands and binding sites
- SGV · Sangivamycin · ligand · chains A
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- V9G · 7-methyl-guanosine-5'-triphosphate-5'-(2'-O-methyl)-adenosine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 8 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
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 | 327 | 0.55 | 0.75 | 41 | SGV, GTA, SAH, V9G |
| 2 | 127 | 0.50 | 0.80 | 19 | EDO |
| 3 | 61 | 0.37 | 0.79 | 20 | empty |
| 4 | 51 | 0.30 | 0.76 | 12 | empty |
| 5 | 53 | 0.25 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 960 Ų buried · 10 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 9EMV · PDBe 9EMV · UniProt P0DTD1
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