2X15

THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 1,3-BISPHOSPHOGLYCERATE

Structural Biology Knowledgebase: 2X15 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2X15

Classification: TRANSFERASE

Total Structure Weight: 45952.59

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOGLYCERATE KINASE 1 A 416 Homo sapiens EC#: 2.7.2.3 IUBMB
Details: COMPLEXED WITH ADP AND 1,3-BPG
Gene Name(s): PGK1 Gene View PGKA MIG10 OK/SW-cl.110

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-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)
X15
Query on X15

A 1,3-BISPHOSPHOGLYCERIC ACID
C3 H8 O10 P2
LJQLQCAXBUHEAZ-UWTATZPHSA-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: 2.1 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.192
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 38.73 α = 90.00
b = 91.75 β = 90.00
c = 108.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-12-21
  • Released Date: 2011-02-09
  • Deposition author(s): Bowler, M.W., Cliff, M.J., Marston, J.P.M., Baxter, N.J., Hounslow, 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