MolNFT v1 · #135629 · protein
Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and ubiquitin S31
5U4P: “Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and ubiquitin S31”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.77). MolNFT v1 #135629 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U4P
- Type
- protein
- Length
- 412 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome regulatory subunit RPN8; 26S proteasome regulatory subunit RPN11…
- EC
- 3.4.19.12
- UniProt
- Q08723, P43588, P05759
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN8 | protein | 177 | 25% helix, 33% strand | Q08723 |
| B | 26S proteasome regulatory subunit RPN11 (EC 3.4.19.12) | protein | 159 | 29% helix, 36% strand | P43588 |
| C | Ubiquitin-40S ribosomal protein S31 | protein | 76 | 25% helix, 37% strand | P05759 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.77 | 0.86 | 60 | empty |
| 2 | 148 | 0.48 | 0.78 | 21 | empty |
| 3 | 62 | 0.37 | 0.79 | 15 | empty |
| 4 | 61 | 0.36 | 0.79 | 17 | empty |
| 5 | 64 | 0.34 | 0.77 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2004 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1158 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5U4P · Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and… · 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
- Every structure of UniProt P05759
- Elsewhere: RCSB PDB 5U4P · PDBe 5U4P · UniProt Q08723 · UniProt P43588 · UniProt P05759
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