Human aldose reductase in complex with NADP+ and the inhibitor IDD594 at temperature of 15K

Experimental Data Snapshot

  • Resolution: 0.81 Å
  • R-Value Free: 0.089 
  • R-Value Work: 0.079 
  • R-Value Observed: 0.079 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Ultrahigh-resolution study of protein atomic displacement parameters at cryotemperatures obtained with a helium cryostat.

Petrova, T.Ginell, S.Mitschler, A.Hazemann, I.Schneider, T.Cousido, A.Lunin, V.Y.Joachimiak, A.Podjarny, A.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1535-1544

  • DOI: https://doi.org/10.1107/S0907444906041035
  • Primary Citation of Related Structures:  
    2I16, 2I17

  • PubMed Abstract: 

    Two X-ray data sets for a complex of human aldose reductase (h-AR) with the inhibitor IDD 594 and the cofactor NADP(+) were collected from two different parts of the same crystal to a resolution of 0.81 A at 15 and 60 K using cold helium gas as cryogen. The contribution of temperature to the atomic B values was estimated by comparison of the independently refined models. It was found that although being slightly different for different kinds of atoms, the differences (deltaB) in the isotropic equivalents B of atomic displacement parameters (ADPs) were approximately constant (about 1.7 A(2)) for well ordered atoms as the temperature was increased from 15 to 60 K. The mean value of this difference varied according to the number of non-H atoms covalently bound to the parent atom. Atoms having a B value of higher than 8 A(2) at 15 K showed much larger deviations of deltaB from the average value, which might reflect partial occupancy of atomic sites. An analysis of the anisotropy of ADPs for individual atoms revealed an increase in the isotropy of ADPs with the increase of the temperature from 15 to 60 K. In a separate experiment, a 0.93 A resolution data set was collected from a different crystal of the same complex at 100 K using cold nitrogen as a cryogen. The effects of various errors on the atomic B values were estimated by comparison of the refined models and the temperature-dependent component was inferred. It was found that both decreasing the data redundancy and increasing the resolution cutoff led to an approximately constant increase in atomic B values for well ordered atoms.

  • Organizational Affiliation

    Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldose reductase316Homo sapiensMutation(s): 0 
Gene Names: AKR1B1ALDR1ALR2
EC: (PDB Primary Data), (UniProt), (UniProt), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens)
Explore P15121 
Go to UniProtKB:  P15121
PHAROS:  P15121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LDT BindingDB:  2I16 IC50: min: 3, max: 30 (nM) from 2 assay(s)
-TΔS: min: -2.26e+1, max: 7.99 (kJ/mol) from 3 assay(s)
ΔH: -4.62e+1 (kJ/mol) from 1 assay(s)
ΔG: min: -4.09e+1, max: -3.13e+1 (kJ/mol) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 0.81 Å
  • R-Value Free: 0.089 
  • R-Value Work: 0.079 
  • R-Value Observed: 0.079 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.173α = 90
b = 66.671β = 92.26
c = 47.297γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description