Research workbench
Crystal structure of NSP16-NSP10 from SARS-cov-2 in complex with 7- methyl-gpppa and S-adenosylmethionine.
Analyse Crystal structure of NSP16-NSP10 from SARS-cov-2 in complex with 7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVN
- Type
- protein
- Length
- 422 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
- ADE, SAM, GTA, MGP, ZN, CL, SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 299 | 29% helix, 21% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 123 | 33% helix, 14% strand | P0DTD1 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A
- SAM · S-adenosylmethionine · ligand · chains A
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 14 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, 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 | 436 | 0.60 | 0.75 | 64 | CL, SAM, GTA, SO4 |
| 2 | 70 | 0.39 | 0.79 | 20 | empty |
| 3 | 61 | 0.29 | 0.74 | 13 | empty |
| 4 | 69 | 0.29 | 0.73 | 17 | empty |
| 5 | 58 | 0.27 | 0.73 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 944 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6WVN · Crystal Structure of Nsp16-Nsp10 from SARS-CoV-2 in Complex with 7-methyl-GpppA 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 6WVN · PDBe 6WVN · UniProt P0DTD1
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