MolNFT v1 · #56257 · protein
Complex structure of SARS-cov 3C-like protease with JMF1586
2Z9L · 3C-like proteinase: “Complex structure of SARS-cov 3C-like protease with JMF1586”. X-ray diffraction, 1 ligand (DAZ), 7 pockets (best druggability 0.76). MolNFT v1 #56257 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z9L
- Type
- protein
- Length
- 601 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
- DAZ
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 300 | 24% helix, 30% strand | P59641 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 301 | 26% helix, 29% strand | P59641 |
Ligands and binding sites
- DAZ · diaminozinc · 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
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 | 1042 | 0.76 | 0.78 | 81 | empty |
| 2 | 406 | 0.61 | 0.76 | 60 | DMS |
| 3 | 179 | 0.48 | 0.76 | 31 | empty |
| 4 | 160 | 0.46 | 0.76 | 28 | DMS, DAZ |
| 5 | 134 | 0.41 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1391 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 2Z9L · complex structure of SARS-CoV 3C-like protease with JMF1586 · 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 2Z9L · PDBe 2Z9L · UniProt P59641
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