3LBD - JenaLib

Asymmetric/Biological Unit(hide GO term definitions)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003708	retinoic acid receptor activity	Combining with retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. Retinoic acid is one of the forms of vitamin A.
	GO:0046965	retinoid X receptor binding	Interacting selectively and non-covalently with a retinoid X receptor.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003707	steroid hormone receptor activity	Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0070384	Harderian gland development	The process whose specific outcome is the progression of the Harderian gland over time, from its formation to the mature structure. The Harderian gland is an anterior orbital structure usually associated with the nictitating membrane, and produces and secretes a variety of substances to the eye, depending upon the species.
	GO:0009952	anterior/posterior pattern specification	The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	GO:0060348	bone development	The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
	GO:0060349	bone morphogenesis	The process in which bones are generated and organized.
	GO:0043010	camera-type eye development	The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
	GO:0060070	canonical Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
	GO:0071300	cellular response to retinoic acid	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
	GO:0002063	chondrocyte development	The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.
	GO:0031076	embryonic camera-type eye development	The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure.
	GO:0048048	embryonic eye morphogenesis	The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized.
	GO:0035116	embryonic hindlimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
	GO:0060429	epithelium development	The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
	GO:0060324	face development	The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
	GO:0048732	gland development	The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion.
	GO:0002068	glandular epithelial cell development	The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland.
	GO:0003430	growth plate cartilage chondrocyte growth	The growth of a growth plate cartilage chondrocyte, where growth contributes to the progression of the chondrocyte over time from one condition to another.
	GO:0003417	growth plate cartilage development	The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
	GO:0060173	limb development	The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
	GO:0035264	multicellular organism growth	The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0061037	negative regulation of cartilage development	Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0045596	negative regulation of cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0032331	negative regulation of chondrocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0001843	neural tube closure	The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0043068	positive regulation of programmed cell death	Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0060740	prostate gland epithelium morphogenesis	The process in which the anatomical structures of epithelia of the prostate gland are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
	GO:0008361	regulation of cell size	Any process that modulates the size of a cell.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0031641	regulation of myelination	Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
	GO:0045637	regulation of myeloid cell differentiation	Any process that modulates the frequency, rate or extent of myeloid cell differentiation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048608	reproductive structure development	The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures.
	GO:0032526	response to retinoic acid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
	GO:0060041	retina development in camera-type eye	The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
	GO:0003406	retinal pigment epithelium development	The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells.
	GO:0048384	retinoic acid receptor signaling pathway	The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
	GO:0043401	steroid hormone mediated signaling pathway	A series of molecular signals mediated by a steroid hormone binding to a receptor.
	GO:0060534	trachea cartilage development	The process whose specific outcome is the progression of the tracheal cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (61, 61)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File