Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues

Structure

x-ray diffraction · 5 distinct chains · 51% helix, 20% strand (DSSP).

Ligands and binding sites

• ZJB · (2R,3R,4S,5R)-2-(3-amino-5-methyl-1,4,5,6,8-pentaazaacenaphthylen-1(5H)-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol · ligand · 3 copies · chains A, C, E
• CL · Chloride ion · ion · 2 copies · chains A, C
• GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 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, 5 with a druggability of 0.5 or more.

Interfaces

9 interfaces between chains.

• E–F · 988 Ų buried · 25 hydrogen bonds · protein-protein
• C–D · 959 Ų buried · 25 hydrogen bonds · protein-protein
• A–B · 955 Ų buried · 26 hydrogen bonds · protein-protein
• A–F · 237 Ų buried · 2 hydrogen bonds · protein-protein
• B–F · 210 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 5AQG · Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site… · the same entry in another collection · chain F against F, TM-score 1.00
• Q99933 · AlphaFold monomer V2.0 prediction for bag family molecular chaperone regulator 1 (Q99933) · a predicted model of the same protein · chain B against A, TM-score 0.94
• P11142 · AlphaFold monomer V2.0 prediction for heat shock cognate 71 kda protein (P11142) · a predicted model of the same protein · chain A against A, TM-score 0.82

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 P11142
• Every structure of UniProt Q99933
• Elsewhere: RCSB PDB 5AQG · PDBe 5AQG · UniProt P11142 · UniProt Q99933