› 5scb

X-ray diffraction
1.8Å resolution

Structure of liver pyruvate kinase in complex with anthraquinone derivative 28

Released:
DOI: 10.2210/pdb5scb/pdb
PDB entry 5scb coloured by chain, front view.
PDB entry 5scb coloured by chain, side view.
PDB entry 5scb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase.
Nain-Perez A, Foller Füchtbauer A, Håversen L, Lulla A, Gao C, Matic J, Monjas L, Rodríguez A, Brear P, Kim W, Hyvönen M, Borén J, Mardinoglu A, Uhlen M, Grøtli M
Eur J Med Chem 234 114270 (2022)
PMID: 35290845

Function and Biology Details

Reaction catalysed: 
ATP + pyruvate = ADP + phosphoenolpyruvate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151770 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyruvate kinase PKLR Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 447 amino acids
Theoretical weight: 48.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P30613 (Residues: 34-160, 262-574; Coverage: 77%)
  • Best match: P30613-2 (Residues: 1-129, 231-543)
Gene names: PK1, PKL, PKLR
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand FBP 8 x FBP
Ligand OXL 8 x OXL
Ligand I7V 6 x I7V
Ligand MG 8 x MG
Ligand K 8 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2
Unit cell:
a: 207.633Å b: 112.468Å c: 188.257Å
α: 90° β: 91.98° γ: 90°
R-values:
R R work R free
0.194 0.193 0.219
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes.
Swint-Kruse et al. (2023)
1 more

1 mention without citation

New divergent dynamics in the isotropic to nematic phase transition of liquid crystals measured with 2D IR vibrational echo spectroscopy.
Sokolowsky et al. (2014)