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


This is version 1.3 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate kinase isozymes M1/M2A, B, C, D550Homo sapiensMutation(s): 0 
Gene Names: PKM2PK2PK3PKMOIP3
EC: 2.7.1.40
Find proteins for P14618 (Homo sapiens)
Explore P14618 
Go to UniProtKB:  P14618
NIH Common Fund Data Resources
PHAROS:  P14618
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
G [auth A] , L [auth B] , M [auth B] , N [auth B] , R [auth C] , S [auth C] , W [auth D] , X [auth D] , 
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
 Ligand Interaction
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



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