1E3K | pdb_00001e3k

Human Progesteron Receptor Ligand Binding Domain in complex with the ligand metribolone (R1881)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.343 (Depositor) 
  • R-Value Work: 
    0.217 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1E3K

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations.

Matias, P.M.Donner, P.Coelho, R.Thomaz, M.Peixoto, C.Macedo, S.Otto, N.Joschko, S.Scholz, P.Wegg, A.Basler, S.Schafer, M.Egner, U.Carrondo, M.A.

(2000) J Biological Chem 275: 26164-26171

  • DOI: https://doi.org/10.1074/jbc.M004571200
  • Primary Citation Related Structures: 
    1E3G, 1E3K

  • PubMed Abstract: 

    The crystal structures of the human androgen receptor (hAR) and human progesterone receptor ligand-binding domains in complex with the same ligand metribolone (R1881) have been determined. Both three-dimensional structures show the typical nuclear receptor fold. The change of two residues in the ligand-binding pocket between the human progesterone receptor and hAR is most likely the source for the specificity of R1881 to the hAR. The structural implications of the 14 known mutations in the ligand-binding pocket of the hAR ligand-binding domains associated with either prostate cancer or the partial or complete androgen receptor insensitivity syndrome were analyzed. The effects of most of these mutants could be explained on the basis of the crystal structure.


  • Organizational Affiliation
    • Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780 Oeiras, Portugal.

Macromolecule Content 

  • Total Structure Weight: 60.05 kDa 
  • Atom Count: 4,070 
  • Modeled Residue Count: 500 
  • Deposited Residue Count: 516 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROGESTERONE RECEPTOR
A, B
258Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P06401 (Homo sapiens)
Explore P06401 
Go to UniProtKB:  P06401
PHAROS:  P06401
GTEx:  ENSG00000082175 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06401
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.343 (Depositor) 
  • R-Value Work:  0.217 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.402α = 90
b = 65.011β = 95.65
c = 71.181γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description