2I16

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


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 D Biol Crystallogr 62: 1535-1544

  • DOI: 10.1107/S0907444906041035
  • Structures With Same Primary Citation

  • 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 sapiensMutation(s): 0 
Gene Names: AKR1B1ALDR1ALR2
EC: 1.1.1.21 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.372 (UniProt), 1.1.1.54 (UniProt)
Find proteins for P15121 (Homo sapiens)
Go to UniProtKB:  P15121
NIH Common Fund Data Resources
PHAROS  P15121
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
LDT
Query on LDT

Download CCD File 
A
IDD594
C16 H12 Br F2 N O3 S
JCZUIWYXULSXSW-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LDTΔG:  38.70000076293945   kJ/mol  BindingDB
LDTIC50:  30   nM  BindingDB
LDTΔG:  31.5   kJ/mol  BindingDB
LDTIC50:  3   nM  BindingDB
LDTΔG:  31.299999237060547   kJ/mol  BindingDB
LDTΔH:  46.20000076293945   kJ/mol  BindingDB
LDT-TΔS:  14.6899995803833   kJ/mol  BindingDB
LDT-TΔS:  22.59000015258789   kJ/mol  BindingDB
LDTΔG:  40.900001525878906   kJ/mol  BindingDB
LDT-TΔS:  7.989999771118164   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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