1PSD | pdb_00001psd

THE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PHOSPHOGLYCERATE DEHYDROGENASE

• PDB DOI: https://doi.org/10.2210/pdb1PSD/pdb

• Classification: OXIDOREDUCTASE (NAD(A))
• Organism(s): Escherichia coli K-12
• Mutation(s): No 


• Deposited: 1995-05-02 Released: 1995-07-31 
• Deposition Author(s): Schuller, D.J., Grant, G.A., Banaszak, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.

Schuller, D.J., Grant, G.A., Banaszak, L.J.

(1995) Nat Struct Biol 2: 69-76

• PubMed: 7719856 
• DOI: https://doi.org/10.1038/nsb0195-69
• Primary Citation Related Structures: 
  1PSD


• PubMed Abstract: 
  

  The crystal structure of the phosphoglycerate dehydrogenase from Escherichia coli is unique among dehydrogenases. It consists of three clearly separate domains connected by flexible hinges. The tetramer has approximate 222 symmetry with the principal contacts between the subunits forming between either the nucleotide binding domains or the regulatory domains. Two slightly different subunit conformations are present which vary only in the orientations of the domains. There is a hinge-like arrangement near the active site cleft and the serine effector site is provided by the regulatory domain of each of two subunits. Interdomain flexibility may play a key role in both catalysis and allosteric inhibition.

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Organizational Affiliation: 
• Department of Molecular Biology, University of California, Irvine 92717.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.73 kDa 
• Atom Count: 6,304 
• Modeled Residue Count: 808 
• Deposited Residue Count: 818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)	A, B	409	Escherichia coli K-12	Mutation(s): 0  EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (UniProt)
UniProt
Find proteins for P0A9T0 (Escherichia coli (strain K12)) Explore P0A9T0  Go to UniProtKB:  P0A9T0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SER	D [auth A], F [auth B]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.1	α = 90
b = 146.3	β = 90
c = 53.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-07-31 
Deposition Author(s): Schuller, D.J., Grant, G.A., Banaszak, L.J.

Revision History  

• Version 1.0: 1995-07-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations