2X13

THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 3PHOSPHOGLYCERATE

Structural Biology Knowledgebase: 2X13 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2X13

Classification: TRANSFERASE

Total Structure Weight: 45179.39

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOGLYCERATE KINASE 1 A 416 Homo sapiens EC#: 2.7.2.3 IUBMB
Gene Name(s): PGK1 Gene View PGKA MIG10 OK/SW-cl.110
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3PG
Query on 3PG

A 3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.185
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 38.94 α = 90.00
b = 91.44 β = 90.00
c = 108.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-12-21
  • Released Date: 2010-12-29
  • Deposition author(s): Bowler, M.W., Cliff, M.J., Marston, J.P.M., Baxter, N.J., Hownslow, A.M.H., Varga, A.V., Szabo, J., Vas, M., Blackburn, G.M., Waltho, J.P.

Revision History

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