MolNFT v1 · #51830 · protein
A structural view of the inactivation of the SARS-coronavirus main proteinase by benzotriazole esters
2VJ1 · SARS coronavirus main proteinase: “A structural view of the inactivation of the SARS-coronavirus main proteinase by benzotriazole esters”. X-ray diffraction, 2 ligands (BEZ, XP1), 7 pockets (best druggability 0.78). MolNFT v1 #51830…
- PDB
- 2VJ1
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARS coronavirus main proteinase
- EC
- 3.4.34.-
- UniProt
- A7J8L3
- Ligands
- BEZ, XP1
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SARS coronavirus main proteinase (EC 3.4.34.-) | protein | 300 | 26% helix, 30% strand | A7J8L3 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains A
- XP1 · 4-(dimethylamino)benzoic acid · ligand · chains B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.78 | 0.80 | 84 | DMS |
| 2 | 388 | 0.59 | 0.75 | 61 | empty |
| 3 | 138 | 0.46 | 0.77 | 25 | empty |
| 4 | 136 | 0.41 | 0.74 | 28 | empty |
| 5 | 134 | 0.40 | 0.74 | 28 | BEZ |
Interfaces
1 interface between chains.
- A–B · 1126 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 2VJ1 · A Structural View of the Inactivation of the SARS-Coronavirus Main Proteinase by… · 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 A7J8L3
- Elsewhere: RCSB PDB 2VJ1 · PDBe 2VJ1 · UniProt A7J8L3
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