Research workbench
Crystal structure of the RPN8-RPN11 mpn domain heterodimer, crystal form II
Analyse Crystal structure of the RPN8-RPN11 mpn domain heterodimer, crystal form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OCN
- Type
- protein
- Length
- 918 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
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN8 | protein | 174 | 25% helix, 38% strand | Q08723 |
| B | 26S proteasome regulatory subunit RPN11 | protein | 165 | 27% helix, 32% strand | P43588 |
| C | NB1 | protein | 122 | 5% helix, 53% strand | — |
| D | 26S proteasome regulatory subunit RPN8 | protein | 172 | 23% helix, 36% strand | Q08723 |
| E | 26S proteasome regulatory subunit RPN11 | protein | 162 | 28% helix, 33% strand | P43588 |
| F | NB1 | protein | 123 | 7% helix, 48% strand | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.79 | 0.90 | 56 | empty |
| 2 | 217 | 0.79 | 0.93 | 40 | empty |
| 3 | 219 | 0.58 | 0.80 | 23 | empty |
| 4 | 370 | 0.55 | 0.74 | 51 | empty |
| 5 | 162 | 0.50 | 0.78 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2049 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 2013 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 673 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 626 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 622 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4OCN · Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II · 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 0.95
- P43588 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase RPN11 (P43588) · a predicted model of the same protein · chain E 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 4OCN · PDBe 4OCN · UniProt Q08723 · UniProt P43588
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