3GR4

Activator-Bound Structure of Human Pyruvate Kinase M2

• PDB DOI: https://doi.org/10.2210/pdb3GR4/pdb

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


• Deposited: 2009-03-24 Released: 2009-04-07 
• Deposition Author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.231 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Activator-Bound Structures of Human Pyruvate Kinase M2

Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Inglese, J., Park, H.

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)

Macromolecule Content

• Total Structure Weight: 243.96 kDa 
• Atom Count: 16,503 
• Modelled Residue Count: 2,048 
• Deposited Residue Count: 2,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase isozymes M1/M2	A, B, C, D	550	Homo sapiens	Mutation(s): 0  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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DYY	CA [auth D], G [auth A]	1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine C18 H18 F2 N2 O6 S2 SHWNKRPMUBFWKE-UHFFFAOYSA-N
ADP	N [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
FBP	DA [auth D], E [auth A], O [auth B], X [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
TLA	BA [auth C], EA [auth D], F [auth A], JA [auth D], P [auth B], W [auth B], Y [auth C]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
UNX	AA [auth C], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], Z [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.231 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.275	α = 90
b = 153.206	β = 102.91
c = 93.138	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
MolProbity	model building
prodrg	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-04-07
  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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary