5HOD | pdb_00005hod

Structure of LHX4 transcription factor complexed with DNA

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Homeobox	e5hodD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
A	Homeobox	e5hodA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF00046	Homeodomain (Homeodomain)	Homeodomain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	DNA (5'-D(PCPTPAPAPTPTPAPCPGPCPCPTPAPAPTPTPAPGPGPT)-3')	-	-	-
B	DNA (5'-D(PAPCPCPTPAPAPTPTPAPGPGPCPGPTPAPAPTPTPAPG)-3')	-	-	-
A, D	LIM/homeobox protein Lhx4	sequence-specific DNA binding DNA binding binding nucleic acid binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nucleoside phosphate binding nucleotide binding sequence-specific DNA binding DNA binding binding nucleic acid binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis placenta development regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis placenta development regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death multicellular organismal process cellular developmental process cell differentiation in spinal cord nervous system development generation of neurons multicellular organism development neurogenesis central nervous system neuron differentiation spinal cord development central nervous system development neuron differentiation cell differentiation somatic motor neuron differentiation medial motor column neuron differentiation ventral spinal cord development spinal cord motor neuron differentiation system development axonogenesis cell projection organization motor neuron axon guidance plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process 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 biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process 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 positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR017970	Homeobox, conserved site	Conserved Site
A, D	IPR049594	LIM/homeobox protein Lhx3/4-like, LIM domain 2	Domain
A, D	IPR001781	Zinc finger, LIM-type	Domain
A, D	IPR050453	LIM/homeobox transcription factors	Family
A, D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, D	IPR047956	LIM/homeobox protein Lhx4, LIM domain 1	Domain
A, D	IPR001356	Homeodomain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: Q969G2	short stature-pituitary and cerebellar defects-small sella turcica syndrome panhypopituitarism pituitary hormone deficiency, combined, 1 hypopituitarism pituitary stalk interruption syndrome cancer hypothyroidism due to deficient transcription factors involved in pituitary development or function large cell medulloblastoma septooptic dysplasia congenital hypothyroidism Idiopathic Hypogonadotropic Hypogonadism medulloblastoma intellectual disability ovarian cancer

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.