MolNFT v1 · #114746 · protein
Crystal structure of ibv papain-like protease plpro C101S mutant in complex with ubiquitin
5BZ0 · Replicase polyprotein 1AB: “Crystal structure of ibv papain-like protease plpro C101S mutant in complex with ubiquitin”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #114746 on GenesisL1: 3D…
- PDB
- 5BZ0
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB; Ubiquitin-40S ribosomal protein S27A
- EC
- 3.4.22.-, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P0C6Y1, P62992
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB (EC 3.4.22.-, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 248 | 26% helix, 36% strand | P0C6Y1 |
| B | Ubiquitin-40S ribosomal protein S27A | protein | 76 | 24% helix, 34% strand | P62992 |
Ligands and binding sites
- ZN · Zinc ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.68 | 0.81 | 48 | empty |
| 2 | 131 | 0.50 | 0.80 | 22 | empty |
| 3 | 59 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1291 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (engineered).
Compared structures
- 5BZ0 · Crystal structure of IBV papain-like protease PLpro C101S 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 0.93
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 P0C6Y1
- Every structure of UniProt P62992
- Elsewhere: RCSB PDB 5BZ0 · PDBe 5BZ0 · UniProt P0C6Y1 · UniProt P62992
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