MolNFT v1 · #102129 · protein
Crystal structure of the RPN8-RPN11 mpn domain heterodimer, crystal form ib
4OCM · 26S proteasome regulatory subunit RPN8: “Crystal structure of the RPN8-RPN11 mpn domain heterodimer, crystal form ib”. X-ray diffraction, 2 ligands (ZN, K), 13 pockets (best druggability 0.83). MolNFT v1 #102129 on GenesisL1: 3D…
- PDB
- 4OCM
- Type
- protein
- Length
- 941 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, K
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit RPN8 | protein | 164 | 29% helix, 32% strand | Q08723 |
| B | 26S proteasome regulatory subunit RPN11 | protein | 177 | 38% helix, 31% strand | P43588 |
| C, F | NB1 | protein | 125 | 7% helix, 51% strand | — |
| D | 26S proteasome regulatory subunit RPN8 | protein | 166 | 30% helix, 37% strand | Q08723 |
| E | 26S proteasome regulatory subunit RPN11 | protein | 184 | 34% helix, 28% strand | P43588 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.83 | 0.95 | 35 | empty |
| 2 | 261 | 0.81 | 0.93 | 41 | empty |
| 3 | 140 | 0.51 | 0.80 | 32 | empty |
| 4 | 248 | 0.47 | 0.73 | 40 | empty |
| 5 | 119 | 0.44 | 0.77 | 22 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1992 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1962 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 651 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 613 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4OCM · Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib · 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 D 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 4OCM · PDBe 4OCM · UniProt Q08723 · UniProt P43588
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