4P6X | pdb_00004p6x

Crystal Structure of cortisol-bound glucocorticoid receptor ligand binding domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8033332	3001442	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8033332	3001442	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8033332	3001442	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8033332	3001442	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8033332	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8033332	3001442	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
K	AAA_23	e4p6xK1	A: alpha arrays	X: DEATH domain	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: AAA_23	ECOD (v295.2)
I	AAA_23	e4p6xI1	A: alpha arrays	X: DEATH domain	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: AAA_23	ECOD (v295.2)
G	AAA_23	e4p6xG1	A: alpha arrays	X: DEATH domain	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: AAA_23	ECOD (v295.2)
E	AAA_23	e4p6xE1	A: alpha arrays	X: DEATH domain	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: AAA_23	ECOD (v295.2)
C	AAA_23	e4p6xC1	A: alpha arrays	X: DEATH domain	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: AAA_23	ECOD (v295.2)
A	AAA_23	e4p6xA1	A: alpha arrays	X: DEATH domain	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: AAA_23	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
I	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
G	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
E	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
C	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF00104	Ligand-binding domain of nuclear hormone receptor (Hormone_recep)	Ligand-binding domain of nuclear hormone receptor	This all helical domain is involved in binding the hormone in these receptors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	Nuclear receptor coactivator 2	protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity transcription regulator activity transcription coregulator activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity transcription regulator activity transcription coregulator activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding transcription coactivator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding protein dimerization activity signaling receptor binding aryl hydrocarbon receptor binding	regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development positive regulation of biological process tissue development positive regulation of developmental process regulation of adipose tissue development anatomical structure development positive regulation of multicellular organismal process regulation of multicellular organismal process animal gross anatomical part developmental process cellular response to stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to stimulus response to hormone response to endogenous stimulus response to chemical cellular response to hormone stimulus carboxylic acid transport transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport establishment of localization organic acid transport localization monocarboxylic acid transport macromolecule localization negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription intracellular receptor signaling pathway intracellular signal transduction peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II behavior circadian behavior locomotory behavior rhythmic behavior locomotor rhythm cellular response to nitrogen compound response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound regulation of cellular response to insulin stimulus cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex nuclear body
A, C, E, G, I A, C, E, G, I, K	Glucocorticoid receptor	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding promoter-specific chromatin binding steroid hormone binding steroid binding lipid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding promoter-specific chromatin binding steroid hormone binding steroid binding lipid binding hormone binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding estrogen response element binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription factor binding protein binding TBP-class protein binding general transcription initiation factor binding nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity nuclear steroid receptor activity nuclear glucocorticoid receptor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity Hsp90 protein binding heat shock protein binding RNA binding kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular process cell division cell cycle chromosome segregation cell cycle process apoptotic process cell death programmed cell death cellular response to stimulus response to lipid response to stimulus response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus cellular process cell division cell cycle chromosome segregation cell cycle process apoptotic process cell death programmed cell death cellular response to stimulus response to lipid response to stimulus response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus cellular response to hormone stimulus RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process response to ketone cellular response to ketone cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid response to dexamethasone regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process miRNA transcription positive regulation of biosynthetic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process regulation of miRNA transcription negative regulation of biological process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of transcription by RNA polymerase II cellular component organization chromatin organization cellular component organization or biogenesis cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to growth factor defense response response to stress inflammatory response neuroinflammatory response intracellular receptor signaling pathway signaling hormone-mediated signaling pathway intracellular signal transduction cell communication signal transduction nuclear receptor-mediated steroid hormone signaling pathway steroid hormone receptor signaling pathway nuclear receptor-mediated signaling pathway developmental process multicellular organismal process myeloid leukocyte differentiation cellular developmental process hemopoiesis macrophage differentiation cell development mononuclear cell differentiation nervous system development multicellular organism development neurogenesis central nervous system development gliogenesis glial cell differentiation myeloid cell differentiation cell differentiation microglia differentiation anatomical structure development animal gross anatomical part developmental process system development leukocyte differentiation astrocyte differentiation behavior motor behavior trans-synaptic signaling synaptic transmission, glutamatergic cell-cell signaling chemical synaptic transmission synaptic signaling anterograde trans-synaptic signaling	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm cytosol chromatin chromosome cytoskeleton spindle microtubule cytoskeleton mitochondrion centrosome microtubule organizing center protein-containing complex synapse cell junction mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
B, D, F, H, J B, D, F, H, J, L	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR017426	Nuclear receptor coactivator	Family
B, D, F, H, J B, D, F, H, J, L	IPR056193	Nuclear receptor coactivator 1-3, bHLH domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR013767	PAS fold	Domain
B, D, F, H, J B, D, F, H, J, L	IPR000014	PAS domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
B, D, F, H, J B, D, F, H, J, L	IPR035965	PAS domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR028822	Nuclear receptor coactivator 2, basic helix-loop-helix	Domain
B, D, F, H, J B, D, F, H, J, L	IPR032565	Nuclear receptor coactivator 2/3, DUF4927	Domain
B, D, F, H, J B, D, F, H, J, L	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, C, E, G, I A, C, E, G, I, K	IPR050200	Nuclear hormone receptor family NR3 subfamily	Family
A, C, E, G, I A, C, E, G, I, K	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR001409	Glucocorticoid receptor	Family
A, C, E, G, I A, C, E, G, I, K	IPR001723	Nuclear hormone receptor	Family
A, C, E, G, I A, C, E, G, I, K	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L	: Q15596	breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm testicular germ cell tumor breast cancer endogenous depression glioblastoma medulloblastoma plasma cell myeloma
A, C, E, G, I A, C, E, G, I, K	: P04150	glucocorticoid resistance endometriosis potassium deficiency disease ocular hypertension psoriasis atrial fibrillation 46,XX disorder of sex development melancholia ulcerative colitis schizophrenia hypokalemia cocaine abuse plasma cell myeloma endogenous depression cocaine dependence glucocorticoid resistance endometriosis potassium deficiency disease ocular hypertension psoriasis atrial fibrillation 46,XX disorder of sex development melancholia ulcerative colitis schizophrenia hypokalemia cocaine abuse plasma cell myeloma endogenous depression cocaine dependence obstructive lung disease bipolar disorder schizoaffective disorder hypertensive disorder prostate cancer sympathetic ophthalmia otitis externa exanthem keratitis Crohn disease temporal arteritis ovarian cancer eye disease autoimmune hemolytic anemia pulmonary fibrosis thyroiditis perennial allergic rhinitis bacterial conjunctivitis granuloma annulare blepharoconjunctivitis rhinitis dermatitis herpetiformis trichinosis acute lymphoblastic leukemia polymyalgia rheumatica breast cancer scalp dermatosis Diamond-Blackfan anemia seasonal allergic rhinitis multiple sclerosis vasomotor rhinitis alopecia areata proctitis skin disease neurotic disorder anterior uveitis inherited aplastic anemia epicondylitis aspiration pneumonitis pseudohermaphroditism iridocyclitis congenital adrenal hyperplasia synovitis atopic conjunctivitis psoriatic arthritis juvenile idiopathic arthritis atypical teratoid rhabdoid tumor pulmonary emphysema large cell medulloblastoma tendinitis pancreatic intraductal papillary-mucinous carcinoma autoimmune thrombocytopenic purpura punctate epithelial keratoconjunctivitis lung cancer dacryocystitis tinea corporis rheumatic heart disease medulloblastoma depressive disorder hemorrhoid rosacea dermatophytosis of groin and perianal area tuberculosis Addison disease breast carcinoma mood disorder allergic asthma hyperaldosteronism Burkitt lymphoma schizophreniform disorder seborrheic dermatitis musculoskeletal system disease ductal breast carcinoma in situ allergic rhinitis primary cutaneous T-cell lymphoma idiopathic acute eosinophilic pneumonia angioedema inflammatory bowel disease choroiditis chronic obstructive pulmonary disease eosinophilic esophagitis anxiety disorder intrinsic asthma erythema multiforme asthma iritis contact dermatitis osteosarcoma atopic eczema corneal ulcer systemic lupus erythematosus extrinsic allergic alveolitis autoimmune disease pulmonary eosinophilia lichen planus tenosynovitis pemphigus B-cell chronic lymphocytic leukemia major depressive disorder tinea pedis gout rheumatoid arthritis acquired thrombocytopenia pneumocystosis sarcoidosis miliary tuberculosis adrenocortical insufficiency Hodgkins lymphoma bronchitis uveitis allergic bronchopulmonary aspergillosis bursitis mycosis fungoides primitive neuroectodermal tumor Sjogren syndrome nephrotic syndrome ankylosing spondylitis chronic beryllium disease Stevens-Johnson syndrome eosinophilic pneumonia aphthous stomatitis invasive ductal breast carcinoma

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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.