6Y1P

Human Aldose Reductase Mutant L300/301A in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid)

• PDB DOI: https://doi.org/10.2210/pdb6Y1P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-02-13 Released: 2021-02-24 
• Deposition Author(s): Hubert, L.-S., Ley, M., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.123 
• R-Value Work: 0.112 
• R-Value Observed: 0.112 

Starting Model: experimental

Literature

Human Aldose Reductase Mutant L300/301A in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid)

Hubert, L.-S., Ley, M., Scheer, F., Diederich, W., Heine, A., Klebe, G.

To be published.

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: 37.44 kDa 
• Atom Count: 3,356 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member B1	A	316	Homo sapiens	Mutation(s): 2  Gene Names: AKR1B1, ALDR1, ALR2 EC: 1.1.1.300 (PDB Primary Data), 1.1.1.372 (PDB Primary Data), 1.1.1.54 (PDB Primary Data), 1.1.1.21 (PDB Primary Data)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
4G7 (Subject of Investigation/LOI)	B [auth A], C [auth A]	3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid C17 H14 F N O6 NEABINVPHSWADT-UHFFFAOYSA-N
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4G7	BindingDB:  6Y1P	-TΔS: -1.10e+1 (kJ/mol) from 1 assay(s)
		ΔH: -3.64e+1 (kJ/mol) from 1 assay(s)
		ΔG: -2.54e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.123 
• R-Value Work: 0.112 
• R-Value Observed: 0.112 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.373	α = 90
b = 66.863	β = 92.339
c = 49.296	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Hubert, L.-S., Ley, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description