Research workbench
Structure of SARS-cov-2 NSP16/NSP10 complex in presence of S-adenosyl- L-homocysteine (sah)
Analyse Structure of SARS-cov-2 NSP16/NSP10 complex in presence of S-adenosyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LW4
- Type
- protein
- Length
- 412 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, ZN
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 298 | 27% helix, 21% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 114 | 24% helix, 13% strand | P0DTD1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- ACT · Acetate ion · additive · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- 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
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 | 171 | 0.50 | 0.78 | 30 | SAH |
| 2 | 172 | 0.49 | 0.76 | 20 | empty |
| 3 | 74 | 0.41 | 0.79 | 15 | empty |
| 4 | 84 | 0.38 | 0.77 | 15 | empty |
| 5 | 60 | 0.35 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 901 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7LW4 · Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of S-adenosyl-L-homocysteine (SAH) · 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 7LW4 · PDBe 7LW4 · UniProt P0DTD1
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