3GQY

Activator-Bound Structure of Human Pyruvate Kinase M2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase isozymes M1/M2
A, B, C, D
550Homo sapiensMutation(s): 0 
Gene Names: PKM2PK2PK3PKM
EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens)
Explore P14618 
Go to UniProtKB:  P14618
GTEx:  ENSG00000067225 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14618
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DZG
Query on DZG

Download Ideal Coordinates CCD File 
H [auth B],
O [auth C]
1-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)-4-[(4-methoxyphenyl)sulfonyl]piperazine
C19 H22 N2 O7 S2
HMGDKYUJSFVHIY-UHFFFAOYSA-N
FBP
Query on FBP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
P [auth C],
T [auth D]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
TLA
Query on TLA

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F [auth A]
J [auth B]
K [auth B]
Q [auth C]
U [auth D]
F [auth A],
J [auth B],
K [auth B],
Q [auth C],
U [auth D],
V [auth D]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
G [auth A]
L [auth B]
M [auth B]
N [auth B]
R [auth C]
G [auth A],
L [auth B],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
W [auth D],
X [auth D],
Y [auth D]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.149α = 90
b = 152.952β = 103.28
c = 93.159γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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