MolNFT v1 · #102014 · protein
Zinc-free RPN11 in complex with RPN8
4O8Y · 26S proteasome regulatory subunit RPN8: “Zinc-free RPN11 in complex with RPN8”. X-ray diffraction, 4 pockets (best druggability 0.80). MolNFT v1 #102014 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4O8Y
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome regulatory subunit RPN8; 26S proteasome regulatory subunit RPN11
- UniProt
- Q08723, P43588
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN8 | protein | 174 | 30% helix, 36% strand | Q08723 |
| B | 26S proteasome regulatory subunit RPN11 | protein | 166 | 30% helix, 32% strand | P43588 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.80 | 0.90 | 52 | EDO |
| 2 | 103 | 0.39 | 0.76 | 19 | EDO |
| 3 | 95 | 0.36 | 0.74 | 14 | EDO |
| 4 | 90 | 0.35 | 0.75 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 2128 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4O8Y · Zinc-free Rpn11 in complex with Rpn8 · 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 0.95
- 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 0.94
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 4O8Y · PDBe 4O8Y · UniProt Q08723 · UniProt P43588
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