Research workbench
Crystal structure of NSP16-NSP10 heterodimer from SARS-cov-2 with 7- methyl-gpppa and S-adenosyl-L-homocysteine in the active site and sulfates in the mRNA binding groove.
Analyse Crystal structure of NSP16-NSP10 heterodimer from SARS-cov-2 with 7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WRZ
- Type
- protein
- Length
- 417 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, MGP, ZN, SO4, CL
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 299 | 29% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 118 | 31% 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
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- CL · Chloride ion · ion · 4 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 | 384 | 0.59 | 0.76 | 53 | SAH, GTA, SO4 |
| 2 | 75 | 0.43 | 0.80 | 20 | empty |
| 3 | 78 | 0.34 | 0.75 | 19 | CL |
| 4 | 85 | 0.32 | 0.74 | 24 | SO4 |
| 5 | 70 | 0.32 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 958 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6WRZ · Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 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 6WRZ · PDBe 6WRZ · UniProt P0DTD1
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