Research workbench
Crystal structure of SARS-cov papain-like protease plpro in complex with ubiquitin aldehyde
Analyse Crystal structure of SARS-cov papain-like protease plpro 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
- 4MM3
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Papain-like proteinase
- EC
- 3.4.19.12, 3.4.22.69
- UniProt
- P0CG48, P0C6U8
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 76 | 25% helix, 36% strand | P0CG48 |
| B | Papain-like proteinase (EC 3.4.19.12, 3.4.22.69) | protein | 316 | 24% helix, 34% strand | P0C6U8 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.69 | 0.82 | 57 | empty |
| 2 | 107 | 0.64 | 0.89 | 23 | empty |
| 3 | 84 | 0.53 | 0.84 | 16 | empty |
| 4 | 79 | 0.44 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1040 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4MM3 · Crystal structure of SARS-CoV papain-like protease PLpro in complex with ubiquitin… · 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 P0CG48
- Every structure of UniProt P0C6U8
- Elsewhere: RCSB PDB 4MM3 · PDBe 4MM3 · UniProt P0CG48 · UniProt P0C6U8
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