Research workbench
Crystal structure of NSP16-NSP10 heterodimer from SARS-cov-2 in complex with 7-methyl-gpppa and S-adenosyl-L-homocysteine.
Analyse Crystal structure of NSP16-NSP10 heterodimer from SARS-cov-2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WQ3
- Type
- protein
- Length
- 418 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
- SAH, GTA, 8NK, ZN, SO4
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 28% 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 | 119 | 27% helix, 14% strand | P0DTD1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A
- 8NK · 7-methylguanosine 5'-diphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.57 | 0.76 | 48 | SAH, GTA, SO4 |
| 2 | 78 | 0.39 | 0.78 | 20 | empty |
| 3 | 53 | 0.38 | 0.80 | 15 | SO4 |
| 4 | 79 | 0.32 | 0.74 | 16 | SO4 |
| 5 | 63 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 969 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6WQ3 · Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with… · the same entry in another collection · chain B against B, 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 6WQ3 · PDBe 6WQ3 · UniProt P0DTD1
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