Research workbench
Crystal structure of the biportin PDR6 in complex with UBC9
Analyse Crystal structure of the biportin PDR6 in complex with UBC9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q83
- Type
- protein
- Length
- 1,168 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Importin beta-like protein KAP122; UBC9
- UniProt
- P32767, P50623
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Importin beta-like protein KAP122 | protein | 1012 | 72% helix, 0% strand | P32767 |
| B | UBC9 | protein | 156 | 35% helix, 21% strand | P50623 |
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.76 | 0.78 | 85 | empty |
| 2 | 150 | 0.72 | 0.90 | 29 | empty |
| 3 | 841 | 0.71 | 0.76 | 84 | empty |
| 4 | 344 | 0.68 | 0.82 | 38 | empty |
| 5 | 187 | 0.62 | 0.83 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1560 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6Q83 · Crystal structure of the biportin Pdr6 in complex with UBC9 · the same entry in another collection · chain A against A, TM-score 1.00
- P50623 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P50623) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P32767 · AlphaFold monomer V2.0 prediction for importin beta-like protein KAP122 (P32767) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P32767
- Every structure of UniProt P50623
- Elsewhere: RCSB PDB 6Q83 · PDBe 6Q83 · UniProt P32767 · UniProt P50623
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