Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.06 kDa 
• Atom Count: 2864 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

1T40

Crystal structure of human aldose reductase complexed with NADP and IDD552 at ph 5

• PDB DOI: 10.2210/pdb1T40/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-04-28 Released: 2004-08-03 
• Deposition Author(s): Ruiz, F., Hazemann, I., Mitschler, A., Chevrier, B., Schneider, T., Joachimiak, A., Karplus, M., Podjarny, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Literature

The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48.

Ruiz, F., Hazemann, I., Mitschler, A., Joachimiak, A., Schneider, T., Karplus, M., Podjarny, A.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1347-1354

• PubMed: 15272156 
• DOI: 10.1107/S0907444904011370
• Primary Citation of Related Structures:  
  1T40, 1T41


• PubMed Abstract: 
  

The X-ray crystal structure of human aldose reductase (ALR2) in complex with the inhibitor IDD552 was determined using crystals obtained from two crystallization conditions with different pH values (pH 5 and 8). In both structures the charged carboxylic head of the inhibitor binds to the active site, making hydrogen-bond interactions with His110 and Tyr48 and electrostatic interactions with NADP+. There is an important difference between the two structures: the observation of a double conformation of the carboxylic acid moiety of the inhibitor at pH 8, with one water molecule interacting with the main configuration. This is the first time that a water molecule has been observed deep inside the ALR2 active site. Furthermore, in the configuration with the lower occupancy factor the difference electron-density map shows a clear peak (2.5sigma) for the H atom in the hydrogen bond between the inhibitor's carboxylic acid and the Tyr48 side-chain O atom. The position of this peak implies that this H atom is shared between both O atoms, indicating possible direct proton transfer from this residue to the inhibitor. This fact agrees with the model of the catalytic mechanism, in which the proton is donated by the Tyr48 hydroxyl to the substrate. These observations are useful both in drug design and in understanding the ALR2 mechanism.

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Organizational Affiliation: 

UPR de Biologie Structurale, IGBMC, CNRS INSERM ULP, 1 Rue Laurent Fries, BP 163, 67404 Illkirch, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1, ALDR1, ALR2 EC: 1.1.1.21 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.372 (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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ID5	C [auth A]	[5-FLUORO-2-({[(4,5,7-TRIFLUORO-1,3-BENZOTHIAZOL-2-YL)METHYL]AMINO}CARBONYL)PHENOXY]ACETIC ACID C17 H10 F4 N2 O4 S ZCAGEXZTORJQDZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ID5	BindingDB:  1T40	IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50	α = 90
b = 67.24	β = 92.5
c = 47.78	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-28 
• Released Date: 2004-08-03 
Deposition Author(s): Ruiz, F., Hazemann, I., Mitschler, A., Chevrier, B., Schneider, T., Joachimiak, A., Karplus, M., Podjarny, A.

Revision History  

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description