6JFB

Crystal structure of human pyruvate kinase M2 isoform

• PDB DOI: https://doi.org/10.2210/pdb6JFB/pdb

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


• Deposited: 2019-02-08 Released: 2020-04-01 
• Deposition Author(s): Chen, T.J., Wang, W.C.
• Funding Organization(s): Ministry of Science and Technology (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.251 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Crystal structure of human pyruvate kinase M2 isoform

Chen, T.J., Wang, W.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 241.98 kDa 
• Atom Count: 16,478 
• Modelled Residue Count: 2,082 
• Deposited Residue Count: 2,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM Isoform M2	A, B, C, D	552	Homo sapiens	Mutation(s): 0  Gene Names: PKM, OIP3, PK2, PK3, PKM2 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
SER	E [auth A], G [auth B], I [auth C], K [auth D]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
PO4	F [auth A], H [auth B], J [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.251 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.763	α = 90
b = 152.573	β = 97.88
c = 94.405	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Chen, T.J., Wang, W.C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references