Research workbench
Crystal structure of SARS-cov-2 main protease (NSP5) in complex with compound 1
Analyse Crystal structure of SARS-cov-2 main protease (NSP5) in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B2U
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase NSP5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- SQ5
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- SQ5 · (5S)-5-(cyclohexylmethyl)-3-(5-fluoropyridin-3-yl) imidazolidine-2,4-dione · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.76 | 0.79 | 83 | empty |
| 2 | 189 | 0.55 | 0.80 | 27 | SQ5 |
| 3 | 325 | 0.54 | 0.74 | 48 | empty |
| 4 | 172 | 0.52 | 0.79 | 26 | SQ5 |
| 5 | 137 | 0.40 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1604 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7B2U · Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 1 · 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 7B2U · PDBe 7B2U · UniProt P0DTD1
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