5GNJ | pdb_00005gnj

Structure of a transcription factor and DNA complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth I]	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	SCOP2B (2022-06-29)
J [auth F]	SCOP2 Family	HLH, helix-loop-helix DNA-binding domain	8070292	4000913	SCOP2 (2022-06-29)
J [auth F]	SCOP2 Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	SCOP2 (2022-06-29)
I [auth E]	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	SCOP2B (2022-06-29)
A [auth G]	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8070293	3001962	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)
B [auth I]	HLH	e5gnjI1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
N	HLH	e5gnjN1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
M	HLH	e5gnjM1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
J [auth F]	HLH	e5gnjF1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
I [auth E]	HLH	e5gnjE1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
F [auth B]	HLH	e5gnjB1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
E [auth A]	HLH	e5gnjA1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
A [auth G]	HLH	e5gnjG1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], J [auth F], M, N	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L], H [auth D], L [auth J], P	DNA (5'-D(TPGPGPGPTPCPAPCPGPTPGPTPTPCP*C)-3')	-	-	-
C [auth K], G [auth C], K [auth H], O	DNA (5'-D(APGPGPAPAPCPAPCPGPTPGPAPCPCP*C)-3')	-	-	-
A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], J [auth F], M, N	Transcription factor MYC2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity protein binding kinase binding enzyme binding protein dimerization activity	regulation of cellular process RNA metabolic process regulation of primary 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 regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary 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 regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of molecular function biosynthetic process regulation of DNA-binding transcription factor activity cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process response to acid chemical response to stimulus response to stress response to chemical response to oxygen-containing compound response to abiotic stimulus response to water response to desiccation response to water deprivation regulation of defense response regulation of response to biotic stimulus defense response to insect biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to other organism defense response response to external stimulus response to biotic stimulus regulation of response to stimulus regulation of response to stress regulation of defense response to insect response to external biotic stimulus response to lipid response to jasmonic acid response to hormone response to fatty acid response to endogenous stimulus cellular response to stimulus abscisic acid-activated signaling pathway signaling hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus signal transduction cellular response to hormone stimulus cellular response to abscisic acid stimulus response to abscisic acid response to alcohol cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol cellular response to lipid protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis aromatic amino acid metabolic process oxoacid metabolic process carboxylic acid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process L-tryptophan metabolic process small molecule metabolic process cellular response to nitrogen compound cellular response to ATP response to organophosphorus response to nitrogen compound response to ATP response to purine-containing compound extracellular ATP signaling flavonoid metabolic process positive regulation of biological process positive regulation of metabolic process regulation of flavonoid biosynthetic process flavonoid biosynthetic process positive regulation of biosynthetic process positive regulation of flavonoid biosynthetic process positive regulation of cellular process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process indole glucosinolate metabolic process glucosinolate metabolic process carbohydrate derivative metabolic process indole glucosinolate biosynthetic process sulfur compound biosynthetic process indole-containing compound biosynthetic process glucosinolate biosynthetic process S-glycoside biosynthetic process sulfur compound metabolic process regulation of small molecule metabolic process regulation of L-tryptophan metabolic process regulation of amino acid metabolic process response to wounding positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process plant-type cell wall organization or biogenesis regulation of cell wall organization or biogenesis cell wall organization or biogenesis regulation of cellular component biogenesis plant-type cell wall biogenesis cell wall biogenesis plant-type secondary cell wall biogenesis regulation of secondary cell wall biogenesis developmental process multicellular organism development multicellular organismal process stomatal complex development plant epidermis development anatomical structure development post-embryonic development tissue development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], J [auth F], M, N	IPR025610	Transcription factor MYC/MYB N-terminal	Domain
A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], J [auth F], M, N	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], J [auth F], M, N	IPR045084	Transcription factor AIB/MYC-like	Family
A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], A [auth G], B [auth I], E [auth A], F [auth B], I [auth E], J [auth F], M, N	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily

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.