Research workbench
Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome
Analyse Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DWZ
- Type
- protein
- Length
- 598 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome non-ATPase regulatory subunit 10; 26S protease regulatory subunit 6B
- UniProt
- Q9Z2X2, Q63570
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 26S proteasome non-ATPase regulatory subunit 10 | protein | 226 | 53% helix, 0% strand | Q9Z2X2 |
| B, D | 26S protease regulatory subunit 6B | protein | 73 | 59% helix, 3% strand | Q63570 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.52 | 0.77 | 19 | empty |
| 2 | 149 | 0.52 | 0.80 | 22 | empty |
| 3 | 123 | 0.46 | 0.78 | 21 | empty |
| 4 | 123 | 0.43 | 0.77 | 28 | empty |
| 5 | 88 | 0.33 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1269 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1255 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 738 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2DWZ · Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Z2X2 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 10… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q63570 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 6B (Q63570) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9Z2X2
- Every structure of UniProt Q63570
- Elsewhere: RCSB PDB 2DWZ · PDBe 2DWZ · UniProt Q9Z2X2 · UniProt Q63570
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.