4UDD

GR in complex with desisobutyrylciclesonide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints.

Edman, K.Hosseini, A.Bjursell, M.K.Aagaard, A.Wissler, L.Gunnarsson, A.Kaminski, T.Kohler, C.Backstrom, S.Jensen, T.J.Cavallin, A.Karlsson, U.Nilsson, E.Lecina, D.Takahashi, R.Grebner, C.Geschwindner, S.Lepisto, M.Hogner, A.C.Guallar, V.

(2015) Structure 23: 2280

  • DOI: 10.1016/j.str.2015.09.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Steroid receptor drugs have been available for more than half a century, but details of the ligand binding mechanism have remained elusive. We solved X-ray structures of the glucocorticoid and mineralocorticoid receptors to identify a conserved plast ...

    Steroid receptor drugs have been available for more than half a century, but details of the ligand binding mechanism have remained elusive. We solved X-ray structures of the glucocorticoid and mineralocorticoid receptors to identify a conserved plasticity at the helix 6-7 region that extends the ligand binding pocket toward the receptor surface. Since none of the endogenous ligands exploit this region, we hypothesized that it constitutes an integral part of the binding event. Extensive all-atom unbiased ligand exit and entrance simulations corroborate a ligand binding pathway that gives the observed structural plasticity a key functional role. Kinetic measurements reveal that the receptor residence time correlates with structural rearrangements observed in both structures and simulations. Ultimately, our findings reveal why nature has conserved the capacity to open up this region, and highlight how differences in the details of the ligand entry process result in differential evolutionary constraints across the steroid receptors.


    Organizational Affiliation

    Discovery Sciences, AstraZeneca, Mölndal, Pepparedsleden 1, 43183 Mölndal, Sweden. Electronic address: karl.edman@astrazeneca.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOCORTICOID RECEPTOR
A
280Homo sapiensMutation(s): 4 
Gene Names: NR3C1 (GRL)
Find proteins for P04150 (Homo sapiens)
Go to Gene View: NR3C1
Go to UniProtKB:  P04150
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR RECEPTOR COACTIVATOR 2
B
14Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CV7
Query on CV7

Download SDF File 
Download CCD File 
A
DESISOBUYTYRYL CICLESONIDE
C28 H38 O6
OXPLANUPKBHPMS-ZXBNPROVSA-N
 Ligand Interaction
CPS
Query on CPS

Download SDF File 
Download CCD File 
A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
CHAPS
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.200α = 90.00
b = 87.200β = 90.00
c = 102.887γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references
  • Version 1.2: 2015-12-16
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Data collection