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 1PL7 | pdb_00001pl7

Human Sorbitol Dehydrogenase (apo)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.234 (Depositor) 
  • R-Value Work: 
    0.200 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1PL7

This is version 1.3 of the entry. See complete history. 

Literature

X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase.

Pauly, T.A., Ekstrom, J.L., Beebe, D.A., Chrunyk, B., Cunningham, D., Griffor, M., Kamath, A., Lee, S.E., Madura, R., Mcguire, D., Subashi, T., Wasilko, D., Watts, P., Mylari, B.L., Oates, P.J., Adams, P.D., Rath, V.L.

(2003) Structure 11: 1071-1085

  • DOI: https://doi.org/10.1016/s0969-2126(03)00167-9
  • Primary Citation Related Structures: 
    1PL6, 1PL7, 1PL8

  • PubMed Abstract: 

    Sorbitol dehydrogenase (hSDH) and aldose reductase form the polyol pathway that interconverts glucose and fructose. Redox changes from overproduction of the coenzyme NADH by SDH may play a role in diabetes-induced dysfunction in sensitive tissues, making SDH a therapeutic target for diabetic complications. We have purified and determined the crystal structures of human SDH alone, SDH with NAD(+), and SDH with NADH and an inhibitor that is competitive with fructose. hSDH is a tetramer of identical, catalytically active subunits. In the apo and NAD(+) complex, the catalytic zinc is coordinated by His69, Cys44, Glu70, and a water molecule. The inhibitor coordinates the zinc through an oxygen and a nitrogen atom with the concomitant dissociation of Glu70. The inhibitor forms hydrophobic interactions to NADH and likely sterically occludes substrate binding. The structure of the inhibitor complex provides a framework for developing more potent inhibitors of hSDH.


  • Organizational Affiliation: 
    • Exploratory Medicinal Sciences, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA.

Macromolecule Content 

  • Total Structure Weight: 153.18 kDa 
  • Atom Count: 12,009 
  • Modeled Residue Count: 1,424 
  • Deposited Residue Count: 1,424 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sorbitol dehydrogenase
A, B, C, D
356Homo sapiensMutation(s): 0 
EC: 1.1.1.14 (PDB Primary Data), 1.1.1.4 (UniProt), 1.1.1 (UniProt), 1.1.1.9 (UniProt), 1.1.1.56 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00796 (Homo sapiens)
Explore Q00796 
Go to UniProtKB:  Q00796
PHAROS:  Q00796
GTEx:  ENSG00000140263 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00796
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.234 (Depositor) 
  • R-Value Work:  0.200 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.946α = 90
b = 134.946β = 90
c = 224.686γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    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: 2024-02-14
    Changes: Data collection, Database references, Derived calculations