3H6O

Activator-Bound Structure of Human Pyruvate Kinase M2

Structural Biology Knowledgebase: 3H6O SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.247

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3H6O

Classification: TRANSFERASE

Total Structure Weight: 242217.75

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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
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)
D8G
Query on D8G

B, C 6-(2-fluorobenzyl)-2,4-dimethyl-4,6-dihydro- 5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin- 5-one
C17 H14 F N3 O S
IEWYEWDDQWYJLU-UHFFFAOYSA-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: 2.0 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.247
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 81.34 α = 90.00
b = 155.69 β = 108.04
c = 101.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-04-23
  • Released Date: 2009-05-05
  • 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: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4