6G4L

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
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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 


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
17-beta-hydroxysteroid dehydrogenase 14270Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BPX1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
B [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
F45
Query on F45
Download Ideal Coordinates CCD File 
E [auth A][6-(3,4-dihydroxyphenyl)pyridin-2-yl](4-fluoro-3-hydroxyphenyl)methanone
C18 H12 F N O4
USZFAGSFWNNZLX-UHFFFAOYSA-N
BGC
Query on BGC
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D [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
F45 BindingDB:  6G4L Ki: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.423α = 90
b = 91.423β = 90
c = 132.141γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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