Research workbench
Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1
Analyse Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HD3
- Type
- protein
- Length
- 885 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Arabidopsis thaliana
- Molecule
- Cell division control protein 48 homolog A
- UniProt
- P54609
- Ligands
- ADP, PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 48 homolog A | protein | 450 | 35% helix, 22% strand | P54609 |
| C | Cell division control protein 48 homolog A | protein | 435 | 35% helix, 23% strand | P54609 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.76 | 0.80 | 80 | PO4 |
| 2 | 264 | 0.62 | 0.81 | 34 | empty |
| 3 | 441 | 0.61 | 0.76 | 48 | empty |
| 4 | 390 | 0.58 | 0.75 | 40 | empty |
| 5 | 263 | 0.53 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–C · 859 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6HD3 · Common mode of remodeling aaa atpases P97/CDC48 by their disassembly cofactors ASPL/PUX1 · the same entry in another collection · chain A against A, TM-score 1.00
- P54609 · AlphaFold monomer V2.0 prediction for cell division control protein 48 homolog a (P54609) · a predicted model of the same protein · chain C against A, TM-score 0.71
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 P54609
- Elsewhere: RCSB PDB 6HD3 · PDBe 6HD3 · UniProt P54609
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.