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.

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), 0.224 (DCC)
R-Value Observed:
0.222 (Depositor)

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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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04150
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75376
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
29M Query on 29M Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

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), 0.224 (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

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Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.