Research workbench
Allosteric opening of the polypeptide-binding site when an HSP70 binds ATP
Analyse Allosteric opening of the polypeptide-binding site when an HSP70 binds ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JNE
- Type
- protein
- Length
- 1,200 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HSP70 chaperone dnak
- UniProt
- P0A6Y8
- Ligands
- ATP, MG, SO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HSP70 chaperone dnak | protein | 600 | 43% helix, 29% strand | P0A6Y8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.83 | 0.87 | 84 | MG, ATP |
| 2 | 771 | 0.78 | 0.82 | 58 | SO4, GOL |
| 3 | 242 | 0.73 | 0.88 | 44 | MG, ATP |
| 4 | 472 | 0.69 | 0.80 | 41 | empty |
| 5 | 223 | 0.68 | 0.86 | 29 | GOL |
Interfaces
1 interface between chains.
- A–B · 1767 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4JNE · Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A6Y8
- Elsewhere: RCSB PDB 4JNE · PDBe 4JNE · UniProt P0A6Y8
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