4B2D

human PKM2 with L-serine and FBP bound.

• PDB DOI: https://doi.org/10.2210/pdb4B2D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-13 Released: 2012-10-10 
• Deposition Author(s): Chaneton, B., Hillmann, P., Zheng, L., Martin, A.C.L., Maddocks, O.D.K., Chokkathukalam, A., Coyle, J.E., Jankevics, A., Holding, F.P., Vousden, K.H., Frezza, C., O'Reilly, M., Gottlieb, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 241.16 kDa 
• Atom Count: 16,952 
• Modelled Residue Count: 2,068 
• Deposited Residue Count: 2,192 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE KINASE ISOZYMES M1/M2	A, B, C	548	Homo sapiens	Mutation(s): 0  EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens) Explore P14618  Go to UniProtKB:  P14618
PHAROS:  P14618 GTEx:  ENSG00000067225

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE KINASE ISOZYMES M1/M2	D	548	Homo sapiens	Mutation(s): 0  EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens) Explore P14618  Go to UniProtKB:  P14618
PHAROS:  P14618 GTEx:  ENSG00000067225

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBP	F [auth A], I [auth B], K [auth C], N [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
SER	E [auth A], H [auth B], J [auth C], M [auth D]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
MG	G [auth A], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SER	Binding MOAD:  4B2D	Kd: 2.00e+5 (nM) from 1 assay(s)
	PDBBind:  4B2D	Kd: 2.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.611	α = 90
b = 151.098	β = 102.01
c = 91.791	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
CSEARCH	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Chaneton, B., Hillmann, P., Zheng, L., Martin, A.C.L., Maddocks, O.D.K., Chokkathukalam, A., Coyle, J.E., Jankevics, A., Holding, F.P., Vousden, K.H., Frezza, C., O'Reilly, M., Gottlieb, E.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-10-24
  Changes: Database references
• Version 1.2: 2012-11-21
  Changes: Database references
• Version 1.3: 2013-02-06
  Changes: Atomic model, Derived calculations, Other
• Version 1.4: 2018-02-07
  Changes: Database references, Structure summary
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.6: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary