2PZN | pdb_00002pzn

The crystallographic structure of Aldose Reductase IDD393 complex confirms Leu300 as a specificity determinant

• PDB DOI: https://doi.org/10.2210/pdb2PZN/pdb

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


• Deposited: 2007-05-18 Released: 2008-05-27 
• Deposition Author(s): Ruiz, F., Hazemann, I., Darmanin, C., Mitschler, A., Van Zandt, M., Joachimiak, A., El-Kabbani, O., Podjarny, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.149 (DCC) 
• R-Value Work: 
  0.128 (DCC) 

Starting Model: experimental

Literature

The Crystallographic Structure of Alr2-Idd393 Complex Confirms Leu300 as a Specificity Determinant

Ruiz, F., Hazemann, I., Darmanin, C., Mitschler, A., Van Zandt, M., Joachimiak, A., El-Kabbani, O., Podjarny, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.01 kDa 
• Atom Count: 3,437 
• 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  Gene Names: ALDR1 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
393	C [auth A]	(5-CHLORO-2-{[(3-NITROBENZYL)AMINO]CARBONYL}PHENOXY)ACETIC ACID C16 H13 Cl N2 O6 VABIMMIJVWNHFI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
393	BindingDB:  2PZN	Kd: 14 (nM) from 1 assay(s)
		IC50: 6 (nM) from 1 assay(s)
		ΔG: min: -5.40e+1, max: 36.89 (kJ/mol) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.149 (DCC) 
• R-Value Work:  0.128 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.224	α = 67.58
b = 47.154	β = 76.47
c = 40.316	γ = 76.11

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
Propietary	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Ruiz, F., Hazemann, I., Darmanin, C., Mitschler, A., Van Zandt, M., Joachimiak, A., El-Kabbani, O., Podjarny, A.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description