6XUM | pdb_00006xum

Human Aldose Reductase Mutant L300/301A in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid)

PDB DOI: https://doi.org/10.2210/pdb6XUM/pdb

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

Deposited: 2020-01-20 Released: 2021-02-03
Deposition Author(s): Hubert, L.-S., Ley, M., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.97 Å
R-Value Free:
0.128 (Depositor), 0.130 (DCC)
R-Value Work:
0.119 (Depositor), 0.120 (DCC)
R-Value Observed:
0.119 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Human Aldose Reductase Mutant L300/301A in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid)

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

To be published.

Macromolecule Content

Total Structure Weight: 37.1 kDa
Atom Count: 3,216
Modeled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
30L (Subject of Investigation/LOI) Query on 30L Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	{5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid C₁₆ H₁₃ F N₂ O₆ HOFFXZBMYHZMTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.97 Å
R-Value Free: 0.128 (Depositor), 0.130 (DCC)
R-Value Work: 0.119 (Depositor), 0.120 (DCC)
R-Value Observed: 0.119 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.288	α = 90
b = 66.739	β = 92.22
c = 49.378	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.