3GR4

Activator-Bound Structure of Human Pyruvate Kinase M2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DYY
Query on DYY

Download Ideal Coordinates CCD File 
CA [auth D], G [auth A]1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine
C18 H18 F2 N2 O6 S2
SHWNKRPMUBFWKE-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
N [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
FBP
Query on FBP

Download Ideal Coordinates CCD File 
DA [auth D], E [auth A], O [auth B], X [auth C]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 
BA [auth C], EA [auth D], F [auth A], JA [auth D], P [auth B], W [auth B], Y [auth C]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth C] , FA [auth D] , GA [auth D] , H [auth A] , HA [auth D] , I [auth A] , IA [auth D] , J [auth A] , 
AA [auth C],  FA [auth D],  GA [auth D],  H [auth A],  HA [auth D],  I [auth A],  IA [auth D],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  Z [auth C]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.275α = 90
b = 153.206β = 102.91
c = 93.138γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MolProbitymodel building
prodrgrefinement

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