8HMQ

Crystal Structure of PKM2 mutant P403A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and mechanistic insights into cancer patient-derived mutations in Pyruvate Kinase muscle isoform 2

Upadhyay, S.Kumar, A.Patel, A.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase PKM
A, B, C, D
551Homo sapiensMutation(s): 1 
Gene Names: PKMOIP3PK2PK3PKM2
EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens)
Explore P14618 
Go to UniProtKB:  P14618
PHAROS:  P14618
GTEx:  ENSG00000067225 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14618
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FBP (Subject of Investigation/LOI)
Query on FBP

Download Ideal Coordinates CCD File 
AA [auth D],
O [auth B],
V [auth C]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D]
DA [auth D]
F [auth A]
G [auth A]
P [auth B]
BA [auth D],
DA [auth D],
F [auth A],
G [auth A],
P [auth B],
Q [auth B],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B],
U [auth C],
Z [auth D]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth D],
H [auth A],
I [auth A],
J [auth A],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
K [auth A]
L [auth A]
M [auth A]
EA [auth D],
FA [auth D],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.829α = 90
b = 136.839β = 90
c = 149.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/RLF/Re-entry/57/2012

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection