Research workbench
Crystal structure of SARS-cov 3C-like protease in apo form
Analyse Crystal structure of SARS-cov 3C-like protease in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VB3
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6U8
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 301 | 26% helix, 30% strand | P0C6U8 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 306 | 25% helix, 29% strand | P0C6U8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.76 | 0.80 | 74 | PEG, EDO |
| 2 | 478 | 0.65 | 0.77 | 69 | empty |
| 3 | 62 | 0.61 | 0.91 | 24 | empty |
| 4 | 164 | 0.47 | 0.76 | 21 | empty |
| 5 | 181 | 0.45 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1415 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3VB3 · Crystal structure of SARS-CoV 3C-like protease in apo form · the same entry in another collection · chain B against B, 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 3VB3 · PDBe 3VB3 · UniProt P0C6U8
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