1M2Z

Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to dexamethasone and a TIF2 coactivator motif

PDB DOI: https://doi.org/10.2210/pdb1M2Z/pdb

Classification: HORMONE/HORMONE ACTIVATOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2002-06-26 Released: 2003-07-15
Deposition Author(s): Bledsoe, R.B., Montana, V.G., Stanley, T.B., Delves, C.J., Apolito, C.J., Mckee, D.D., Consler, T.G., Parks, D.J., Stewart, E.L., Willson, T.M., Lambert, M.H., Moore, J.T., Pearce, K.H., Xu, H.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.267
R-Value Work: 0.237
R-Value Observed: 0.267

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 66.18 kDa
Atom Count: 4,782
Modelled Residue Count: 550
Deposited Residue Count: 556
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucocorticoid receptor	A, C [auth D]	257	Homo sapiens	Mutation(s): 1
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04150
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nuclear receptor coactivator 2	B, D [auth E]	21	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DEX Query on DEX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth D]	H [auth A], I [auth D]	DEXAMETHASONE C₂₂ H₂₉ F O₅ UREBDLICKHMUKA-CXSFZGCWSA-N		Interactions Focus chain H [auth A] Focus chain I [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth D]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
DEX	BindingDB: 1M2Z	Ki: min: 0.69, max: 6.8 (nM) from 9 assay(s)
		Kd: min: 2, max: 19 (nM) from 3 assay(s)
		IC50: min: 0.5, max: 22 (nM) from 29 assay(s)
		EC50: min: 0.1, max: 17 (nM) from 18 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.267
R-Value Work: 0.237
R-Value Observed: 0.267
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.843	α = 90
b = 125.843	β = 90
c = 85.976	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNX	refinement
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-07-15
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Data collection
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.5: 2021-10-27
Changes: Database references, Structure summary
Version 1.6: 2024-02-14
Changes: Data collection
Version 1.7: 2024-04-03
Changes: Refinement description