Research workbench
Crystal structure of SARS-cov papain-like protease C112S mutant in complex with ubiquitin
Analyse Crystal structure of SARS-cov papain-like protease C112S mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M0W
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1A; Ubiquitin
- EC
- 3.4.19.12, 3.4.22.69
- UniProt
- P0C6U8, P62992
- Ligands
- ZN, NA
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1A (EC 3.4.19.12, 3.4.22.69) | protein | 317 | 26% helix, 37% strand | P0C6U8 |
| B | Ubiquitin | protein | 76 | 20% helix, 34% strand | P62992 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.71 | 0.82 | 54 | empty |
| 2 | 94 | 0.42 | 0.78 | 19 | empty |
| 3 | 104 | 0.42 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1031 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4M0W · Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain B against A, TM-score 0.96
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
- Every structure of UniProt P62992
- Elsewhere: RCSB PDB 4M0W · PDBe 4M0W · UniProt P0C6U8 · UniProt P62992
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