2R24 | pdb_00002r24

Human Aldose Reductase structure

• PDB DOI: https://doi.org/10.2210/pdb2R24/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-08-24 Released: 2008-12-23 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.291 (Depositor) 
• R-Value Work: 
  0.257 (Depositor) 
• R-Value Observed: 
  0.260 (Depositor) 

Literature

Quantum model of catalysis based on 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

• PubMed: 18250329 
• 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.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.06 kDa 
• Atom Count: 2,882 
• Modeled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(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

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
LDT	C [auth A]	IDD594 C16 H12 Br F2 N O3 S JCZUIWYXULSXSW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LDT	BindingDB:  2R24	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: 1.75 Å
• R-Value Free:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.291 (Depositor) 
• R-Value Work:  0.257 (Depositor) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.066	α = 90
b = 67.126	β = 92.41
c = 47.862	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
LAUEGEN	data reduction
LSCALE	data scaling
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-27
  Changes: Data collection
• Version 1.3: 2012-03-14
  Changes: Database references, Structure summary
• Version 1.4: 2018-04-25
  Changes: Data collection
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Derived calculations