MolNFT v1 · #138088 · protein
RPN8/RPN11 dimer complex
5W83 · 26S proteasome regulatory subunit RPN8: “RPN8/RPN11 dimer complex”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.81). MolNFT v1 #138088 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W83
- Type
- protein
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome regulatory subunit RPN8; Ubiquitin carboxyl-terminal hydrolase RPN11
- EC
- 3.4.19.12
- UniProt
- Q08723, P43588
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN8 | protein | 173 | 27% helix, 33% strand | Q08723 |
| B | Ubiquitin carboxyl-terminal hydrolase RPN11 (EC 3.4.19.12) | protein | 158 | 37% helix, 34% strand | P43588 |
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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.81 | 0.93 | 39 | empty |
| 2 | 107 | 0.39 | 0.76 | 20 | empty |
| 3 | 52 | 0.39 | 0.82 | 21 | empty |
| 4 | 92 | 0.37 | 0.75 | 15 | empty |
| 5 | 84 | 0.35 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2175 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5W83 · Rpn8/Rpn11 dimer complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q08723 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN8 (Q08723) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P43588 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase RPN11 (P43588) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q08723
- Every structure of UniProt P43588
- Elsewhere: RCSB PDB 5W83 · PDBe 5W83 · UniProt Q08723 · UniProt P43588
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