8X4R | pdb_00008x4r

Pyruvate kinase M2 (PKM2) mutant in complex with phenylalanine

• PDB DOI: https://doi.org/10.2210/pdb8X4R/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-11-15 Released: 2024-11-20 
• Deposition Author(s): Wang, W.C., Su, T.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.201 (DCC) 

Starting Model: experimental

Literature

Pyruvate kinase M2 (PKM2) mutant in complex with phenylalanine

Wang, W.C., Su, T.H.

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: 232.3 kDa 
• Atom Count: 15,984 
• Modeled Residue Count: 2,014 
• Deposited Residue Count: 2,124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM	A, B, C, D	531	Homo sapiens	Mutation(s): 4  Gene Names: PKM EC: 2.7.11.1 (UniProt), 2.7.10.2 (UniProt), 2.7.1.40 (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
PHE (Subject of Investigation/LOI)	F [auth A], H [auth B], K [auth D]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
K	E [auth A], G [auth B], I [auth C], J [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.201 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.142	α = 90
b = 69.399	β = 106.536
c = 168.818	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: 2024-11-20 
Deposition Author(s): Wang, W.C., Su, T.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	107-2321-B-007 -005 -

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release