Research workbench
Crystal structure of SARS-cov-2 NSP10/NSP16 in complex with the WZ16 inhibitor
Analyse Crystal structure of SARS-cov-2 NSP10/NSP16 in complex with the WZ16 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R1U
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-O-methyltransferase NSP16; Non-structural protein 10
- EC
- 2.1.1.57
- UniProt
- P0DTD1
- Ligands
- 4IK, GTA, ZN
- Pockets
- 6 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase NSP16 (EC 2.1.1.57) | protein | 297 | 29% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 113 | 21% helix, 15% strand | P0DTD1 |
Ligands and binding sites
- 4IK · (2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic acid · ligand · chains A
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- 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
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.46 | 0.79 | 20 | empty |
| 2 | 154 | 0.44 | 0.75 | 29 | 4IK |
| 3 | 63 | 0.34 | 0.77 | 15 | empty |
| 4 | 53 | 0.30 | 0.75 | 13 | empty |
| 5 | 63 | 0.27 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7R1U · Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the WZ16 inhibitor · 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 7R1U · PDBe 7R1U · UniProt P0DTD1
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