3O4R | pdb_00003o4r

Crystal Structure of Human Dehydrogenase/Reductase (SDR family) member 4 (DHRS4)

PDB DOI: https://doi.org/10.2210/pdb3O4R/pdb

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

Deposited: 2010-07-27 Released: 2010-08-04
Deposition Author(s): Ugochukwu, E., Bhatia, C., Krojer, T., Vollmar, M., Yue, W.W., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.250 (Depositor), 0.270 (DCC)
R-Value Work:
0.210 (Depositor), 0.230 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Dehydrogenase/Reductase (SDR family) member 4 (DHRS4)

Ugochukwu, E., Bhatia, C., Krojer, T., Vollmar, M., Yue, W.W., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 114.41 kDa
Atom Count: 8,296
Modeled Residue Count: 1,010
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrogenase/reductase SDR family member 4	A, B, C, D	261	Homo sapiens	Mutation(s): 0 Gene Names: DHRS4, UNQ851/PRO1800 EC: 1.1.1.184
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BTZ2 (Homo sapiens) Explore Q9BTZ2 Go to UniProtKB: Q9BTZ2
GTEx: ENSG00000157326
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BTZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], L [auth C], N [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C]	K [auth B], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain K [auth B] Focus chain M [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D]	F [auth A], I [auth B], J [auth B], O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.250 (Depositor), 0.270 (DCC)
R-Value Work: 0.210 (Depositor), 0.230 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.07	α = 90
b = 132.2	β = 90
c = 133.796	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description