MolNFT v1 · #175215 · protein
SARS cov-2 plpro in complex with GRL0617
7CJM · Non-structural protein 3: “SARS cov-2 plpro in complex with GRL0617”. X-ray diffraction, 2 ligands (TTT, ZN), 2 pockets (best druggability 0.48). MolNFT v1 #175215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CJM
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- TTT, ZN
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 316 | 25% helix, 34% strand | P0DTD1 |
Ligands and binding sites
- TTT · 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide · ligand · chains B
- ZN · Zinc ion · metal · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.48 | 0.79 | 24 | TTT |
| 2 | 72 | 0.37 | 0.77 | 20 | empty |
Compared structures
- 7CJM · SARS CoV-2 PLpro in complex with GRL0617 · 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 P0DTD1
- Elsewhere: RCSB PDB 7CJM · PDBe 7CJM · UniProt P0DTD1
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