4AXX

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP 3-phosphoglycerate and beryllium trifluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Catalytic Activity in the Transitions State Analogue Stabilised Conformation of a Phosphoryl Transfer Enzyme

Bowler, M.W.Cliff, M.J.Blackburn, G.M.Waltho, J.P.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOGLYCERATE KINASE 1
A
417Homo sapiensMutation(s): 0 
Gene Names: PGK1 (PGKA)
EC: 2.7.2.3
Find proteins for P00558 (Homo sapiens)
Go to Gene View: PGK1
Go to UniProtKB:  P00558
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3PG
Query on 3PG

Download SDF File 
Download CCD File 
A
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.820α = 90.00
b = 90.800β = 90.00
c = 108.540γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-15 
  • Released Date: 2013-06-26 
  • Deposition Author(s): Bowler, M.W.

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Atomic model, Database references, Other, Structure summary