1PDG - JenaLib

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:87
 aligned with PDGFB_HUMAN | P01127 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:96
                                    99       109       119       129       139       149       159       169       179      
          PDGFB_HUMAN    90 EPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAA 185
               SCOP domains d1pdga_ A: Platelet         -derived growth factor BB                                            SCOP domains
               CATH domains 1pdgA00 A:9-104 Cys         tine-knot cytokines                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeee..---------.....eeeeeeeee.......eeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------P------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------PDGF_1       --------------------------------------------------- PROSITE
               Transcript 1 Exon 1.7  PDB: A:9-71 (gaps) UniProt: 84-152 [INCOMPLETE]      Exon 1.8c  PDB: A:72-104          Transcript 1
                 1pdg A   9 EPAMIAECKTRTEVFEISR---------FLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAA 104
                                    18        |-        38        48        58        68        78        88        98      
                                             27        37

Chain B from PDB  Type:PROTEIN  Length:83
 aligned with PDGFB_HUMAN | P01127 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:94
                                    97       107       117       127       137       147       157       167       177    
          PDGFB_HUMAN    88 IAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCE 181
               SCOP domains d1pdgb_ B: Platelet-           derived growth factor BB                                        SCOP domains
               CATH domains 1pdgB00 B:7-100 Cyst           ine-knot cytokines                                              CATH domains
               Pfam domains PDGF_N-1p------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee.-----------....eeeeeeeee.......eeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) V------------------------------P-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------PDGF_1       ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.7  PDB: B:7-71 (gaps) UniProt: 84-152 [INCOMPLETE]        Exon 1.8c  PDB: B:72-100      Transcript 1
                 1pdg B   7 IAEPAMIAECKTRTEVFEIS-----------LVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCE 100
                                    16        26         - |      46        56        66        76        86        96    
                                              26          38

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with PDGFB_HUMAN | P01127 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:96
                                    97       107       117       127       137       147       157       167       177      
          PDGFB_HUMAN    88 IAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETV 183
               SCOP domains d1pdgc_ C: Platelet-          derived growth factor BB                                           SCOP domains
               CATH domains 1pdgC00 C:7-102 Cyst          ine-knot cytokines                                                 CATH domains
           Pfam domains (1) ---------PDGF-1pdgC0          1 C:16-99                                                      --- Pfam domains (1)
           Pfam domains (2) ---------PDGF-1pdgC0          2 C:16-99                                                      --- Pfam domains (2)
           Pfam domains (3) ---------PDGF-1pdgC0          3 C:16-99                                                      --- Pfam domains (3)
         Sec.struct. author ..........eeeeeeeee.----------.....eeeeeeeee.......eeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) V------------------------------P---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------PDGF_1       ------------------------------------------------- PROSITE
               Transcript 1 Exon 1.7  PDB: C:7-71 (gaps) UniProt: 84-152 [INCOMPLETE]        Exon 1.8c  PDB: C:72-102        Transcript 1
                 1pdg C   7 IAEPAMIAECKTRTEVFEIS----------FLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETV 102
                                    16        26         -|       46        56        66        76        86        96      
                                              26         37

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PDGFB_HUMAN | P01127)

molecular function
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0042056	chemoattractant activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
	GO:0048407	platelet-derived growth factor binding	Interacting selectively and non-covalently with platelet-derived growth factor.
	GO:0005161	platelet-derived growth factor receptor binding	Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0016176	superoxide-generating NADPH oxidase activator activity	Increases the activity of the enzyme superoxide-generating NADPH oxidase.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0032148	activation of protein kinase B activity	Any process that initiates the activity of the inactive enzyme protein kinase B.
	GO:0032147	activation of protein kinase activity	Any process that initiates the activity of an inactive protein kinase.
	GO:0060326	cell chemotaxis	The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0016049	cell growth	The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
	GO:0071363	cellular response to growth factor stimulus	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 growth factor stimulus.
	GO:0071506	cellular response to mycophenolic 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 mycophenolic acid stimulus.
	GO:0001892	embryonic placenta development	The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0030097	hemopoiesis	The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
	GO:0072255	metanephric glomerular mesangial cell development	The process whose specific outcome is the progression of a glomerular mesangial cell in the metanephros over time, from its formation to the mature structure.
	GO:0002548	monocyte chemotaxis	The movement of a monocyte in response to an external stimulus.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0010629	negative regulation of gene expression	Any process that decreases 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:0010512	negative regulation of phosphatidylinositol biosynthetic process	Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phosphatidylinositol.
	GO:0010544	negative regulation of platelet activation	Any process that decreases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:1905064	negative regulation of vascular smooth muscle cell differentiation	Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell differentiation.
	GO:0038001	paracrine signaling	The transfer of information from one cell to another, where the signal travels from the signal-producing cell to the receiving cell by passive diffusion or bulk flow in intercellular fluid. The signaling cell and the receiving cell are usually in the vicinity of each other.
	GO:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0048008	platelet-derived growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
	GO:0050918	positive chemotaxis	The directed movement of a motile cell or organism towards a higher concentration of a chemical.
	GO:2000573	positive regulation of DNA biosynthetic process	Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
	GO:0045740	positive regulation of DNA replication	Any process that activates or increases the frequency, rate or extent of DNA replication.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0043536	positive regulation of blood vessel endothelial cell migration	Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
	GO:0090280	positive regulation of calcium ion import	Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
	GO:0051781	positive regulation of cell division	Any process that activates or increases the frequency, rate or extent of cell division.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0050921	positive regulation of chemotaxis	Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
	GO:0045737	positive regulation of cyclin-dependent protein serine/threonine kinase activity	Any process that activates or increases the frequency, rate or extent of CDK activity.
	GO:0001938	positive regulation of endothelial cell proliferation	Any process that activates or increases the rate or extent of endothelial cell proliferation.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	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:0003104	positive regulation of glomerular filtration	Any process that activates or increases the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule.
	GO:0072126	positive regulation of glomerular mesangial cell proliferation	Any process that increases the frequency, rate or extent of glomerular mesangial cell proliferation.
	GO:1900127	positive regulation of hyaluronan biosynthetic process	Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process.
	GO:2000591	positive regulation of metanephric mesenchymal cell migration	Any process that activates or increases the frequency, rate or extent of metanephric mesenchymal cell migration.
	GO:0035793	positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway	Any process that increases the frequency, rate or extent of metanephric mesenchymal cell migration as a result of the series of molecular signals generated as a consequence of a platelet-derived growth factor receptor-beta binding to one of its physiological ligands.
	GO:0045840	positive regulation of mitotic nuclear division	Any process that activates or increases the frequency, rate or extent of mitosis.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0043552	positive regulation of phosphatidylinositol 3-kinase activity	Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:1902895	positive regulation of pri-miRNA transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter.
	GO:0031954	positive regulation of protein autophosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation by a protein of one or more of its own residues.
	GO:0061098	positive regulation of protein tyrosine kinase activity	Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity.
	GO:2000379	positive regulation of reactive oxygen species metabolic process	Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
	GO:0014911	positive regulation of smooth muscle cell migration	Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
	GO:0048661	positive regulation of smooth muscle cell proliferation	Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:1904754	positive regulation of vascular associated smooth muscle cell migration	Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell migration.
	GO:1905176	positive regulation of vascular smooth muscle cell dedifferentiation	Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell dedifferentiation.
	GO:1904707	positive regulation of vascular smooth muscle cell proliferation	Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell proliferation.
	GO:0070528	protein kinase C signaling	A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0032355	response to estradiol	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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0043627	response to estrogen	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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
	GO:0001666	response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0032868	response to insulin	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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0014070	response to organic cyclic compound	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 an organic cyclic compound stimulus.
	GO:0010033	response to organic substance	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 an organic substance stimulus.
	GO:0009611	response to wounding	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 stimulus indicating damage to the organism.
	GO:0007179	transforming growth factor beta receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (11, 11)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 5)

PROSITE Motifs (1, 3)

Exons (2, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (2, 4)

Gene Ontology (100, 100)

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