MolNFT v1 · #176962 · protein
Crystal structure of the SARS-cov-2 papain-like protease (plpro) C112S mutant bound to compound S43
7E35 · Non-structural protein 3: “Crystal structure of the SARS-cov-2 papain-like protease (plpro) C112S mutant bound to compound S43”. X-ray diffraction, 2 ligands (GYX, ZN), 6 pockets (best druggability 0.89). MolNFT v1 #176962 on…
- PDB
- 7E35
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- 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
- GYX, ZN
- Pockets
- 6 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 287 | 27% helix, 31% strand | P0DTD1 |
| A | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 315 | 27% helix, 35% strand | P0DTD1 |
Ligands and binding sites
- GYX · N-[(3-acetamidophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.89 | 0.91 | 136 | GYX |
| 2 | 63 | 0.72 | 0.97 | 18 | empty |
| 3 | 121 | 0.47 | 0.78 | 21 | empty |
| 4 | 69 | 0.43 | 0.80 | 13 | empty |
| 5 | 61 | 0.39 | 0.80 | 11 | empty |
Interfaces
1 interface between chains.
- B–A · 1306 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7E35 · Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant bound to… · 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 7E35 · PDBe 7E35 · UniProt P0DTD1
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