Research workbench
1.98 ångström resolution crystal structure of NSP16-NSP10 heterodimer from SARS-cov-2 in complex with sinefungin
Analyse 1.98 ångström resolution crystal structure of NSP16-NSP10 heterodimer from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WKQ
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- 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
- SFG, NA, ZN
- Pockets
- 17 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 297 | 29% helix, 23% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 122 | 23% helix, 14% strand | P0DTD1 |
| C | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 294 | 28% helix, 23% strand | P0DTD1 |
| D | Non-structural protein 10 | protein | 116 | 24% helix, 15% strand | P0DTD1 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains B, D
- FMT · Formic acid · additive · 15 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.56 | 0.74 | 51 | empty |
| 2 | 329 | 0.54 | 0.74 | 40 | SFG, FMT |
| 3 | 193 | 0.49 | 0.76 | 36 | SFG, FMT |
| 4 | 183 | 0.48 | 0.76 | 27 | empty |
| 5 | 92 | 0.44 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 963 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 958 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 850 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 563 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6WKQ · 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer from SARS-CoV-2 in… · 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 6WKQ · PDBe 6WKQ · UniProt P0DTD1
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