Research workbench
Complex structure of SARS-cov 3C-like protease with epdtc
Analyse Complex structure of SARS-cov 3C-like protease with epdtc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z9J
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P59641
- Ligands
- DTZ
- Pockets
- 5 · 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 | 302 | 26% helix, 29% strand | P59641 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 304 | 26% helix, 29% strand | P59641 |
Ligands and binding sites
- DTZ · zinc(II)hydrogensulfide · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.76 | 0.78 | 84 | empty |
| 2 | 537 | 0.62 | 0.75 | 77 | empty |
| 3 | 203 | 0.50 | 0.76 | 28 | DMS, DTZ |
| 4 | 173 | 0.44 | 0.75 | 26 | DMS, DTZ |
| 5 | 128 | 0.44 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2Z9J · Complex structure of SARS-CoV 3C-like protease with EPDTC · 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 P59641
- Elsewhere: RCSB PDB 2Z9J · PDBe 2Z9J · UniProt P59641
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