6G4L | pdb_00006g4l

17beta-hydroxysteroid Dehydrogenase Type 14 Mutant Y253A in Complex With a Non-steroidal Inhibitor

PDB DOI: https://doi.org/10.2210/pdb6G4L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2018-03-27 Released: 2019-04-10
Deposition Author(s): Badran, M., Klebe, G., Heine, A., Marchais-Oberwinkler, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.179 (Depositor), 0.178 (DCC)
R-Value Work:
0.156 (Depositor), 0.158 (DCC)
R-Value Observed:
0.158 (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

Mutational and structural studies uncover crucial amino acids determining activity and stability of 17beta-HSD14

Badran, M., Bertoletti, N., Keils, A., Heine, A., Klebe, G., Marchais-Oberwinkler, S.

(2019) J Steroid Biochem Mol Biol

DOI: https://doi.org/10.1016/j.jsbmb.2019.02.009

Macromolecule Content

Total Structure Weight: 29.59 kDa
Atom Count: 2,223
Modeled Residue Count: 253
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
17-beta-hydroxysteroid dehydrogenase 14	A	270	Homo sapiens	Mutation(s): 1 Gene Names: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 EC: 1.1.1 (PDB Primary Data), 1.1.1.122 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BPX1 (Homo sapiens) Explore Q9BPX1 Go to UniProtKB: Q9BPX1
PHAROS: Q9BPX1 GTEx: ENSG00000087076
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BPX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
F45 Query on F45 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	[6-(3,4-dihydroxyphenyl)pyridin-2-yl](4-fluoro-3-hydroxyphenyl)methanone C₁₈ H₁₂ F N O₄ USZFAGSFWNNZLX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
BGC Query on BGC 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]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.44 Å
R-Value Free: 0.179 (Depositor), 0.178 (DCC)
R-Value Work: 0.156 (Depositor), 0.158 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.423	α = 90
b = 91.423	β = 90
c = 132.141	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
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: 2019-04-10

Deposition Author(s):

Badran, M.

Klebe, G.

Heine, A.

Marchais-Oberwinkler, S.

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2020-04-22
Changes: Data collection, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary