Crystal structure of a 17beta-hydroxysteroid dehydrogenase (holo form) from fungus Cochliobolus lunatus in complex with NADPH and coumestrol

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural studies on the flavonoid inhibition of a fungal 17Beta-Hydroxysteroid dehydrogenase

Cassetta, A.Krastanova, I.Kristan, K.Brunskole Svegelj, M.Lamba, D.Lanisnik Rizner, T.Stojan, J.

(2012) Biochem J 441: 151-160

  • DOI: https://doi.org/10.1042/BJ20110567
  • Primary Citation of Related Structures:  
    3QWF, 3QWI

  • PubMed Abstract: 

    The 17β-HSD (17β-hydroxysteroid dehydrogenase) from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) is a NADP(H)-dependent enzyme that preferentially catalyses the interconversion of inactive 17-oxo-steroids and their active 17β-hydroxy counterparts. 17β-HSDcl belongs to the SDR (short-chain dehydrogenase/reductase) superfamily. It is currently the only fungal 17β-HSD member that has been described and represents one of the model enzymes of the cP1 classical subfamily of NADPH-dependent SDR enzymes. A thorough crystallographic analysis has been performed to better understand the structural aspects of this subfamily and provide insights into the evolution of the HSD enzymes. The crystal structures of the 17β-HSDcl apo, holo and coumestrol-inhibited ternary complex, and the active-site Y167F mutant reveal subtle conformational differences in the substrate-binding loop that probably modulate the catalytic activity of 17β-HSDcl. Coumestrol, a plant-derived non-steroidal compound with oestrogenic activity, inhibits 17β-HSDcl [IC50 2.8 μM; at 100 μM substrate (4-oestrene-3,17-dione)] by occupying the putative steroid-binding site. In addition to an extensive hydrogen-bonding network, coumestrol binding is stabilized further by π-π stacking interactions with Tyr212. A stopped-flow kinetic experiment clearly showed the coenzyme dissociation as the slowest step of the reaction and, in addition to the low steroid solubility, it prevents the accumulation of enzyme-coenzyme-steroid ternary complexes.

  • Organizational Affiliation

    Istituto di Cristallografia - UOS Trieste, Consiglio Nazionale delle Ricerche, Area Science Park-Basovizza, S.S. 14 km 163.5, I-34149 Trieste, Italy. alberto.cassetta@ic.cnr.it

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
17beta-hydroxysteroid dehydrogenase
A, B, C, D
270Curvularia lunataMutation(s): 0 
Gene Names: 17HSDcl
Find proteins for O93874 (Cochliobolus lunatus)
Explore O93874 
Go to UniProtKB:  O93874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93874
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
M [auth C],
P [auth D]
C21 H28 N7 O17 P3
Query on CUE

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth D]
C15 H8 O5
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
N [auth C]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth C],
O [auth C],
R [auth D],
S [auth D],
T [auth D]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
CUE Binding MOAD:  3QWI IC50: 2800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.41α = 90
b = 116.81β = 103.14
c = 70.43γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Non-polymer description
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description