5HNU | pdb_00005hnu

Crystal Structure of AKR1C3 complexed with octyl gallate

PDB DOI: https://doi.org/10.2210/pdb5HNU/pdb

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

Deposited: 2016-01-18 Released: 2017-01-25
Deposition Author(s): Li, C., Zhao, Y., Zhang, H., Hu, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.239 (Depositor), 0.247 (DCC)
R-Value Work:
0.195 (Depositor), 0.205 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of AKR1C3 complexed with octyl gallte

Li, C., Zhao, Y., Zhang, H., Hu, X.

To be published.

Macromolecule Content

Total Structure Weight: 73.57 kDa
Atom Count: 5,322
Modeled Residue Count: 630
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C3	A, B [auth C]	315	Homo sapiens	Mutation(s): 0 Gene Names: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS EC: 1.1.1.357 (PDB Primary Data), 1.1.1.112 (PDB Primary Data), 1.1.1.188 (PDB Primary Data), 1.1.1.239 (PDB Primary Data), 1.1.1.64 (PDB Primary Data), 1.3.1.20 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1 (UniProt), 1.1.1.210 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42330 (Homo sapiens) Explore P42330 Go to UniProtKB: P42330
PHAROS: P42330 GTEx: ENSG00000196139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42330
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 E [auth C] SDF format, chain C [auth A] MOL2 format, chain E [auth C] MOL2 format, chain C [auth A] mmCIF format, chain E [auth C] mmCIF format, chain C [auth A]	C [auth A], E [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth C] Interactions & Density Focus chain C [auth A] Focus chain E [auth C]
65D Query on 65D Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	octyl 3,4,5-trihydroxybenzoate C₁₅ H₂₂ O₅ NRPKURNSADTHLJ-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
65D	BindingDB: 5HNU	IC50: min: 2560, max: 9280 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239 (Depositor), 0.247 (DCC)
R-Value Work: 0.195 (Depositor), 0.205 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.666	α = 90
b = 81.826	β = 102.07
c = 76.013	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2024-03-20
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.