2QXW | pdb_00002qxw

Perdeuterated alr2 in complex with idd594

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.80 Å
  • R-Value Free: 
    0.112 (Depositor), 0.108 (DCC) 
  • R-Value Work: 
    0.104 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 
    0.104 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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

Literature

Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase.

Blakeley, M.P., Ruiz, F., Cachau, R., Hazemann, I., Meilleur, F., Mitschler, A., Ginell, S., Afonine, P., Ventura, O.N., Cousido-Siah, A., Haertlein, M., Joachimiak, A., Myles, D., Podjarny, A.

(2008) Proc Natl Acad Sci U S A 105: 1844-1848

  • DOI: https://doi.org/10.1073/pnas.0711659105
  • Primary Citation Related Structures: 
    2QXW, 2R24

  • PubMed Abstract: 

    We present results of combined studies of the enzyme human aldose reductase (h-AR, 36 kDa) using single-crystal x-ray data (0.66 A, 100K; 0.80 A, 15K; 1.75 A, 293K), neutron Laue data (2.2 A, 293K), and quantum mechanical modeling. These complementary techniques unveil the internal organization and mobility of the hydrogen bond network that defines the properties of the catalytic engine, explaining how this promiscuous enzyme overcomes the simultaneous requirements of efficiency and promiscuity offering a general mechanistic view for this class of enzymes.

    • Organizational Affiliation: 
    • Institut Laue Langevin, 6, Rue Jules Horowitz, BP 156, 38042 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 37.44 kDa 
  • Atom Count: 3,560 
  • Modeled Residue Count: 313 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aldose reductase316Homo sapiensMutation(s): 0 
EC: 1.1.1.21 (PDB Primary Data), 1.1.1.372 (UniProt), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens)
Explore P15121 
Go to UniProtKB:  P15121
PHAROS:  P15121
GTEx:  ENSG00000085662 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
LDT BindingDB:  2QXW IC50: min: 3, max: 30 (nM) from 2 assay(s)
ΔG: min: -4.62e+1, max: 7.99 (kJ/mol) from 8 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.80 Å
  • R-Value Free:  0.112 (Depositor), 0.108 (DCC) 
  • R-Value Work:  0.104 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 0.104 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.345α = 90
b = 66.945β = 92.07
c = 47.407γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-29
    Changes: Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description