Crystal of pyruvate kinase (pyk) from mycobacterium tuberculosis in complex with oxalate, soaked with allosteric activators AMP and glucose 6-phosphate

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).

Ligands and binding sites

• AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
• OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
• G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
• K · Potassium ion · metal · chains B
• PO4 · Phosphate ion · ion · 2 copies · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• C–D · 1838 Ų buried · 21 hydrogen bonds · protein-protein
• A–B · 1673 Ų buried · 17 hydrogen bonds · protein-protein
• B–D · 1047 Ų buried · 11 hydrogen bonds · protein-protein
• A–C · 995 Ų buried · 11 hydrogen bonds · protein-protein

Compared structures

• 5WSC · Crystal of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate… · the same entry in another collection · chain B against B, TM-score 1.00
• P9WKE5 · AlphaFold monomer V2.0 prediction for pyruvate kinase (P9WKE5) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P9WKE5
• Elsewhere: RCSB PDB 5WSC · PDBe 5WSC · UniProt P9WKE5