1P8F

A four location model to explain the stereospecificity of proteins.

• PDB DOI: https://doi.org/10.2210/pdb1P8F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-07 Released: 2003-05-20 
• Deposition Author(s): Mesecar, A.D., Koshland Jr., D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

Structural biology: A new model for protein stereospecificity.

Mesecar, A.D., Koshland Jr., D.E.

(2000) Nature 403: 614-615

• PubMed: 10688187 
• DOI: https://doi.org/10.1038/35001144
• Primary Citation of Related Structures:  
  1P8F, 1PB1

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Organizational Affiliation: 

Center for Pharmaceutical Biotechnology, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 60607, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 46.4 kDa 
• Atom Count: 3,490 
• Modelled Residue Count: 416 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A	416	Escherichia coli	Mutation(s): 0  Gene Names: ICD OR ICDA OR ICDE OR B1136 EC: 1.1.1.42
UniProt
Find proteins for P08200 (Escherichia coli (strain K12)) Explore P08200  Go to UniProtKB:  P08200

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ICT	D [auth A]	ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.306	α = 90
b = 103.306	β = 90
c = 150.004	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-20 
Deposition Author(s): Mesecar, A.D., Koshland Jr., D.E.

Revision History  

• Version 1.0: 2003-05-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations