Research workbench
Crystal structure of SARS-cov 3C-like protease with C4Z
Analyse Crystal structure of SARS-cov 3C-like protease with C4Z in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VB5
- Type
- protein
- Length
- 615 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; C4Z inhibitor
- EC
- 3.4.22.-
- UniProt
- P0C6U8
- Ligands
- PHQ
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 301 | 25% helix, 30% strand | P0C6U8 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 306 | 25% helix, 28% strand | P0C6U8 |
| E, F | C4Z inhibitor | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 2 copies · chains A, E, B, F
- EDO · 1,2-ethanediol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.76 | 0.79 | 69 | empty |
| 2 | 79 | 0.68 | 0.94 | 26 | empty |
| 3 | 358 | 0.56 | 0.74 | 49 | empty |
| 4 | 156 | 0.46 | 0.76 | 30 | empty |
| 5 | 175 | 0.44 | 0.74 | 32 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1376 Ų buried · 35 hydrogen bonds · protein-protein
- B–F · 462 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 452 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 20 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 3VB5 · Crystal structure of SARS-CoV 3C-like protease with C4Z · 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 P0C6U8
- Elsewhere: RCSB PDB 3VB5 · PDBe 3VB5 · UniProt P0C6U8
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