Research workbench
Crystal structure of the RPN8-RPN11 mpn domain heterodimer, crystal form ia
Analyse Crystal structure of the RPN8-RPN11 mpn domain heterodimer, crystal form ia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OCL
- Type
- protein
- Length
- 942 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome regulatory subunit RPN8; 26S proteasome regulatory subunit RPN11; NB1
- UniProt
- Q08723, P43588
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN8 | protein | 163 | 27% helix, 36% strand | Q08723 |
| B | 26S proteasome regulatory subunit RPN11 | protein | 181 | 35% helix, 28% strand | P43588 |
| C, F | NB1 | protein | 125 | 7% helix, 51% strand | — |
| D | 26S proteasome regulatory subunit RPN8 | protein | 164 | 26% helix, 34% strand | Q08723 |
| E | 26S proteasome regulatory subunit RPN11 | protein | 184 | 34% helix, 27% strand | P43588 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.81 | 0.93 | 42 | empty |
| 2 | 347 | 0.78 | 0.89 | 56 | empty |
| 3 | 122 | 0.57 | 0.84 | 25 | empty |
| 4 | 156 | 0.54 | 0.80 | 27 | empty |
| 5 | 155 | 0.47 | 0.76 | 25 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2006 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1917 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 681 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 639 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 401 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4OCL · Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia · the same entry in another collection · chain F against F, 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 0.97
- 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 0.88
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 4OCL · PDBe 4OCL · UniProt Q08723 · UniProt P43588
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