2I17

Human aldose reductase in complex with NADP+ and the inhibitor IDD594 at temperature of 60K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.81 Å
  • R-Value Free: 0.091 
  • R-Value Work: 0.076 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 62: 1535-1544

  • DOI: 10.1107/S0907444906041035
  • Primary Citation of Related Structures:  2I16

  • 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 cryog ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldose reductase
A
316Homo sapiensGene Names: AKR1B1 (ALDR1)
EC: 1.1.1.21
Find proteins for P15121 (Homo sapiens)
Go to Gene View: AKR1B1
Go to UniProtKB:  P15121
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
LDT
Query on LDT

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Download CCD File 
A
IDD594
[2-(4-BROMO-2-FLUORO-BENZYLTHIOCARBAMOYL)-5-FLUORO-PHENOXY]-ACETIC ACID
C16 H12 Br F2 N O3 S
JCZUIWYXULSXSW-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

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Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LDTIC50: 3 - 30 nM (99) BINDINGDB
LDTΔG: -31.3 - -40.9 kJ/mol (99) BINDINGDB
LDTΔH: -46.2 kJ/mol (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.81 Å
  • R-Value Free: 0.091 
  • R-Value Work: 0.076 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.214α = 90.00
b = 66.701β = 92.27
c = 47.307γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance