Research workbench
Crystal structure of the SARS-cov-2 main protease in complex with Z- VAD(OME)-fmk
Analyse Crystal structure of the SARS-cov-2 main protease in complex with Z… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C8B
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Z-VAD(OME)-fmk
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- PHQ, CF0, CL
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 26% helix, 29% strand | P0DTD1 |
| D | Z-VAD(OME)-fmk | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains A, D
- CF0 · Fluoromethane · ion · chains A, D
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.47 | 0.84 | 16 | PHQ |
| 2 | 67 | 0.36 | 0.77 | 14 | empty |
| 3 | 63 | 0.32 | 0.76 | 15 | CL |
Interfaces
1 interface between chains.
- A–D · 289 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 7C8B · Crystal structure of the SARS-CoV-2 main protease in complex with Z-VAD(OMe)-FMK · 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 7C8B · PDBe 7C8B · UniProt P0DTD1
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