5JSF

Crystal structure of 17beta-hydroxysteroid dehydrogenase 14 S205 variant in complex with NAD.

• PDB DOI: https://doi.org/10.2210/pdb5JSF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-05-08 Released: 2016-07-13 
• Deposition Author(s): Bertoletti, N., Marchais-Oberwinkler, S., Heine, A., Klebe, G.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.187 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

New Insights into Human 17 beta-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor.

Bertoletti, N., Braun, F., Lepage, M., Moller, G., Adamski, J., Heine, A., Klebe, G., Marchais-Oberwinkler, S.

(2016) J Med Chem 59: 6961-6967

• PubMed: 27362750 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00293
• Primary Citation of Related Structures:  
  5HS6, 5ICM, 5ICS, 5JS6, 5JSF


• PubMed Abstract: 
  

  17β-HSD14 is a SDR enzyme able to oxidize estradiol and 5-androstenediol using NAD(+). We determined the crystal structure of this human enzyme as the holo form and as ternary complexes with estrone and with the first potent, nonsteroidal inhibitor. The structures reveal a conical, rather large and lipophilic binding site and are the starting point for structure-based inhibitor design. The two natural variants (S205 and T205) were characterized and adopt a similar structure.

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Organizational Affiliation: 

Institute for Pharmaceutical Chemistry, Philipps University Marburg , 35037 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.54 kDa 
• Atom Count: 2,090 
• Modelled Residue Count: 268 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
17-beta-hydroxysteroid dehydrogenase 14	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 EC: 1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BPX1 (Homo sapiens) Explore Q9BPX1  Go to UniProtKB:  Q9BPX1
PHAROS:  Q9BPX1 GTEx:  ENSG00000087076

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.187 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.256	α = 90
b = 130.256	β = 90
c = 130.256	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-13 
Deposition Author(s): Bertoletti, N., Marchais-Oberwinkler, S., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	MA-5287/1-1
German Research Foundation	Germany	KL-1204/15-1

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description