3ZRA | pdb_00003zra

Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators

• PDB DOI: https://doi.org/10.2210/pdb3ZRA/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-15 Released: 2011-08-17 
• Deposition Author(s): Lusher, S.J., Raaijmakers, H.C.A., Vu-Pham, D., Dechering, K., Wai Lam, T., Brown, A.R., Hamilton, N.M., Nimz, O., Azevedo, R., McGuire, R., Oubrie, A., de Vlieg, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators.

Lusher, S.J., Raaijmakers, H.C., Vu-Pham, D., Dechering, K., Lam, T.W., Brown, A.R., Hamilton, N.M., Nimz, O., Bosch, R., McGuire, R., Oubrie, A., de Vlieg, J.

(2011) J Biological Chem 286: 35079-35086

• PubMed: 21849509 
• DOI: https://doi.org/10.1074/jbc.M111.273029
• Primary Citation Related Structures: 
  3ZR7, 3ZRA, 3ZRB


• PubMed Abstract: 
  

  The progesterone receptor is able to bind to a large number and variety of ligands that elicit a broad range of transcriptional responses ranging from full agonism to full antagonism and numerous mixed profiles inbetween. We describe here two new progesterone receptor ligand binding domain x-ray structures bound to compounds from a structurally related but functionally divergent series, which show different binding modes corresponding to their agonistic or antagonistic nature. In addition, we present a third progesterone receptor ligand binding domain dimer bound to an agonist in monomer A and an antagonist in monomer B, which display binding modes in agreement with the earlier observation that agonists and antagonists from this series adopt different binding modes.

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Organizational Affiliation: 
• Department of Molecular Design and Informatics, DMPK, MSD, PO Box 20, 5340 BH Oss, The Netherlands. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.85 kDa 
• Atom Count: 4,206 
• Modeled Residue Count: 500 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROGESTERONE RECEPTOR	A, B	260	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P06401 (Homo sapiens) Explore P06401  Go to UniProtKB:  P06401
PHAROS:  P06401 GTEx:  ENSG00000082175

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ORB	C [auth A], E [auth B]	N-{(1R)-1-[4-(2-CHLORO-5-FLUOROPYRIDIN-3-YL)PHENYL]ETHYL}-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE C18 H17 Cl F N3 O3 S UOZIRTCHSJAAOG-SNVBAGLBSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.305	α = 90
b = 64.114	β = 96.53
c = 69.932	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
DTSCALEAVERAGE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Lusher, S.J., Raaijmakers, H.C.A., Vu-Pham, D., Dechering, K., Wai Lam, T., Brown, A.R., Hamilton, N.M., Nimz, O., Azevedo, R., McGuire, R., Oubrie, A., de Vlieg, J.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2011-10-26
  Changes: Database references
• Version 1.2: 2017-12-27
  Changes: Database references, Structure summary
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other