2PZN

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 37.01 kDa
Atom Count: 3,437
Modelled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens) Explore P15121 Go to UniProtKB: P15121
PHAROS: P15121 GTEx: ENSG00000085662
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
393 Query on 393 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(5-CHLORO-2-{[(3-NITROBENZYL)AMINO]CARBONYL}PHENOXY)ACETIC ACID C₁₆ H₁₃ Cl N₂ O₆ VABIMMIJVWNHFI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
393	BindingDB: 2PZN	Kd: 14 (nM) from 1 assay(s)
		IC50: 6 (nM) from 1 assay(s)
		-TΔS: min: -1.25e+1, max: 36.89 (kJ/mol) from 3 assay(s)
		ΔH: -5.40e+1 (kJ/mol) from 1 assay(s)
		ΔG: min: -4.22e+1, max: -3.45e+1 (kJ/mol) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

Revision History (Full details and data files)

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

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2PZN

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)