6H0M

17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide

PDB DOI: https://doi.org/10.2210/pdb6H0M/pdb

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

Deposited: 2018-07-10 Released: 2019-07-31
Deposition Author(s): Badran, M., Klebe, G., Heine, A., Marchais-Oberwinkler, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.147
R-Value Work: 0.126
R-Value Observed: 0.127

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

17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide

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

To be published.

Macromolecule Content

Total Structure Weight: 29.22 kDa
Atom Count: 2,206
Modelled Residue Count: 257
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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), 1.1.1.62 (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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BPX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BGC Query on BGC 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]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.147
R-Value Work: 0.126
R-Value Observed: 0.127
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.59	α = 90
b = 91.59	β = 90
c = 131.112	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

Entry History

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Badran, M.

Klebe, G.

Heine, A.

Marchais-Oberwinkler, S.

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-20
Changes: Structure summary

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Help and Resources

6H0M

17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide

17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)