4MDD | pdb_00004mdd

Crystal Structure of the Glucocorticoid Receptor Bound to a Non-steroidal Antagonist Reveals Repositioning and Partial Disordering of Activation Function Helix 12

• PDB DOI: https://doi.org/10.2210/pdb4MDD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-08-22 Released: 2014-12-03 
• Deposition Author(s): Coghlan, M.J., Luz, J.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal Structure of the Glucocorticoid Receptor Bound to a Non-steroidal Antagonist Reveals Repositioning and Partial Disordering of Activation Function Helix 12

Luz, J.G., Coghlan, M.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.62 kDa 
• Atom Count: 4,141 
• Modeled Residue Count: 492 
• Deposited Residue Count: 546 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	A, B	258	Homo sapiens	Mutation(s): 9  Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150 GTEx:  ENSG00000113580

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor corepressor 1	C, D	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens) Explore O75376  Go to UniProtKB:  O75376
PHAROS:  O75376 GTEx:  ENSG00000141027

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
29M	E [auth A], F [auth B]	N-[2-{[benzyl(methyl)amino]methyl}-3-(4-fluoro-2-methoxyphenyl)-5-(propan-2-yl)-1H-indol-7-yl]methanesulfonamide C28 H32 F N3 O3 S MFAGIEMFDDDLMT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
29M	BindingDB:  4MDD	Ki: 1.2 (nM) from 1 assay(s)
		IC50: min: 2.8, max: 11 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.543	α = 90
b = 72.543	β = 90
c = 229.472	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Coghlan, M.J., Luz, J.G.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations