› 4b2d

X-ray diffraction
2.3Å resolution

human PKM2 with L-serine and FBP bound.

Released:
DOI: 10.2210/pdb4b2d/pdb
PDB entry 4b2d coloured by chain, front view.
PDB entry 4b2d coloured by chain, side view.
PDB entry 4b2d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Serine is a natural ligand and allosteric activator of pyruvate kinase M2.
Chaneton B, Hillmann P, Zheng L, Martin ACL, Maddocks ODK, Chokkathukalam A, Coyle JE, Jankevics A, Holding FP, Vousden KH, Frezza C, O'Reilly M, Gottlieb E
Nature 491 458-462 (2012)
PMID: 23064226

Function and Biology Details

Reactions catalysed: 
ATP + pyruvate = ADP + phosphoenolpyruvate
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146983 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pyruvate kinase PKM Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 548 amino acids
Theoretical weight: 59.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P14618 (Residues: 2-531; Coverage: 100%)
Gene names: OIP3, PK2, PK3, PKM, PKM2
Sequence domains:
Structure domains:
Pyruvate kinase PKM Chain: D
Molecule details ›
Chain: D
Length: 548 amino acids
Theoretical weight: 59.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P14618 (Residues: 2-531; Coverage: 100%)
Gene names: OIP3, PK2, PK3, PKM, PKM2
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SER 4 x SER
Ligand FBP 4 x FBP
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 80.611Å b: 151.098Å c: 91.791Å
α: 90° β: 102.01° γ: 90°
R-values:
R R work R free
0.176 0.174 0.226
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

132 review citations

The Emerging Hallmarks of Cancer Metabolism.
Pavlova et al. (2016)
131 more

12 mentions without citation

Serine is a natural ligand and allosteric activator of pyruvate kinase M2.
Chaneton et al. (2012)
11 more