3G2G

S437Y Mutant of human muscle pyruvate kinase, isoform M2

• PDB DOI: https://doi.org/10.2210/pdb3G2G/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-31 Released: 2009-03-03 
• Deposition Author(s): Hong, B., Dimov, S., Allali-Hassani, A., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, c., Weigelt, J., Bochkarev, A., Vedadi, M., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

S437Y Mutant of human muscle pyruvate kinase, isoform M2

Allali-Hassani, A., Hong, B., Dimov, S., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, c., Weigelt, J., Bochkarev, A., Park, H., Vedadi, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 234.2 kDa 
• Atom Count: 15,165 
• Modelled Residue Count: 1,976 
• Deposited Residue Count: 2,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase isozymes M1/M2	A, B, C, D	533	Homo sapiens	Mutation(s): 1  Gene Names: PKM2, PK2, PK3, PKM EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (UniProt), 2.7.10.2 (UniProt)
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth C], BA [auth C], CA [auth C], E [auth A], F [auth A], K [auth B], KA [auth D], L [auth B], LA [auth D], M [auth B], MA [auth D], NA [auth D], Z [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNX	DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], N [auth B], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], X [auth B], Y [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.546	α = 90
b = 137.885	β = 90
c = 155.684	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Hong, B., Dimov, S., Allali-Hassani, A., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, c., Weigelt, J., Bochkarev, A., Vedadi, M., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description