3GR4

Activator-Bound Structure of Human Pyruvate Kinase M2

Structural Biology Knowledgebase: 3GR4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GR4

Classification: TRANSFERASE

Total Structure Weight: 243961.75

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate kinase isozymes M1/M2 A, B, C, D 550 Homo sapiens EC#: 2.7.1.40 IUBMB
Gene Name(s): PKM Gene View OIP3 PK2 PK3 PKM2

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DYY
Query on DYY

A, D 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 Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FBP
Query on FBP

A, B, C, D BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE (Synonym)
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TLA
Query on TLA

A, B, C, D L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A, B, C, D UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.208
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 81.28 α = 90.00
b = 153.21 β = 102.91
c = 93.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-24
  • Released Date: 2009-04-07
  • Deposition author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4