Research workbench
Severe acute respiratory syndrome-coronavirus papain-like protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation
Analyse Severe acute respiratory syndrome-coronavirus papain-like protease inhibitors… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJ5
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1A
- EC
- 3.4.22.-
- UniProt
- P0C6U8
- Ligands
- GRM, ZN
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1A (EC 3.4.22.-) | protein | 312 | 24% helix, 37% strand | P0C6U8 |
| B | Replicase polyprotein 1A (EC 3.4.22.-) | protein | 262 | 29% helix, 35% strand | P0C6U8 |
Ligands and binding sites
- GRM · N-(1,3-benzodioxol-5-ylmethyl)-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.80 | 0.83 | 78 | GRM |
| 2 | 981 | 0.80 | 0.81 | 92 | GRM |
| 3 | 372 | 0.79 | 0.88 | 49 | empty |
| 4 | 82 | 0.48 | 0.81 | 13 | empty |
| 5 | 98 | 0.46 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1475 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3MJ5 · Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design… · 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 P0C6U8
- Elsewhere: RCSB PDB 3MJ5 · PDBe 3MJ5 · UniProt P0C6U8
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