6cfn

Crystal Structure of the DNA-free Glucocorticoid Receptor DNA Binding Domain

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucocorticoid receptor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 418–506 Author chain B； PDBConstruct 2–90； UniProt 418–506 Author chain C； PDBConstruct 2–90； UniProt 418–506 Author chain D； PDBConstruct 2–90； UniProt 418–506 Author chain E； PDBConstruct 2–90； UniProt 418–506 Author chain F； PDBConstruct 2–90； UniProt 418–506 Author chain G； PDBConstruct 2–90； UniProt 418–506 Author chain H； PDBConstruct 2–90； UniProt 418–506

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6cfn
Deposition date deposition_date	2018-02-15
Structure title title	Crystal Structure of the DNA-free Glucocorticoid Receptor DNA Binding Domain
Keywords keywords	DNA binding domain, nuclear receptor, glucocorticoid receptor, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6cfn__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6cfn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cfn__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	13.64 Å
Rg (electron density)	12.86 Å
Total Rg	14.03 Å
Atom count	626
Residues	80
Excluded volume	11248 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cfn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6cfn__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6cfn__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6cfn__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6cfn__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6cfn__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`6cfn__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`6cfn__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Glucocorticoid receptor
Molecular weight formula_weight	10005.8 kDa
Mutation mutation	UNP Residues 418-506
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	4643

SPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGIQQATTG

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6cfna_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d6cfnb_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d6cfnc_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d6cfnd_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d6cfne_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d6cfnf_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d6cfng_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d6cfnh_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

CATH v4.4 (8 domains)

Domain ID domain_id	6cfnA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	6cfnB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	6cfnC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	6cfnD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	6cfnE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	6cfnF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	6cfnG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	6cfnH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

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Unit-cell length a length_a	65.803 Å
Unit-cell length b length_b	65.432 Å
Unit-cell length c length_c	72.659 Å
Unit-cell angle α angle_alpha	71.27 °
Unit-cell angle β angle_beta	84.96 °
Unit-cell angle γ angle_gamma	68.44 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	36.042 Å
R factor r_factor	0.1973
R_work r_work	0.1946
R_free r_free	0.2483

Crystal Structure of the DNA-free Glucocorticoid Receptor DNA Binding Domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucocorticoid receptor

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6cfn__assembly_1__model_1

6cfn__assembly_1__model_1 | I(q)

6cfn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of the DNA-free Glucocorticoid Receptor DNA Binding Domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucocorticoid receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6cfn__assembly_1__model_1

6cfn__assembly_1__model_1 | I(q)

6cfn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)