8VOI | pdb_00008voi

HADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	SCOP2B Superfamily	vWA-like	8033178	3000832	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	BACK	e8voiB01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: BACK	ECOD (v294.1)
A	BACK	e8voiA01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: BACK	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01091	PTN/MK heparin-binding protein family, C-terminal domain (PTN_MK_C)	PTN/MK heparin-binding protein family, C-terminal domain		Domain
A	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Pleiotrophin	enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding molecular function activator activity enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity glycosaminoglycan binding chondroitin sulfate binding binding carbohydrate derivative binding sulfur compound binding molecular function activator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity carbohydrate binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding kinase binding enzyme binding protein kinase binding heparin binding	negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling cellular response to stimulus multicellular organismal process response to stimulus cell projection organization positive regulation of neuron projection regeneration regulation of cellular response to stress neuron projection development regeneration neuron projection regeneration positive regulation of developmental process multicellular organism development neuron differentiation cell differentiation anatomical structure development positive regulation of cell projection organization response to wounding system development positive regulation of response to wounding developmental process regulation of axon regeneration regulation of cell projection organization response to external stimulus nervous system development generation of neurons regulation of response to stimulus regulation of neuron projection regeneration regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process cellular developmental process regulation of response to external stimulus cell development response to axon injury regulation of response to wounding positive regulation of response to stimulus cellular component organization neurogenesis positive regulation of response to external stimulus cellular response to stress axon regeneration positive regulation of neuron projection development regulation of response to stress response to stress cellular component organization or biogenesis plasma membrane bounded cell projection organization axon development neuron development positive regulation of axon regeneration regulation of plasma membrane bounded cell projection organization regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number stem cell population maintenance behavior system process learning learning or memory nervous system process cognition ossification bone mineralization animal organ development biomineral tissue development tissue development ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process regulation of cell motility endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration cell migration cell motility locomotion dendrite regeneration dendrite development regulation of multicellular organismal development hemopoiesis regulation of cell differentiation regulation of cell development immune system process regulation of hemopoiesis regulation of immune system process tissue regeneration developmental growth growth neuroblast proliferation negative regulation of neural precursor cell proliferation regulation of neuroblast proliferation regulation of neurogenesis negative regulation of neuroblast proliferation regulation of nervous system development negative regulation of neurogenesis negative regulation of cellular process negative regulation of nervous system development negative regulation of cell differentiation regulation of neural precursor cell proliferation negative regulation of cell population proliferation cell population proliferation negative regulation of developmental process negative regulation of cell development regulation of cell population proliferation neural precursor cell proliferation negative regulation of multicellular organismal process memory regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of biomineral tissue development positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification positive regulation of cell division cell division regulation of cell division cell chemotaxis leukocyte chemotaxis involved in inflammatory response chemotaxis defense response leukocyte migration involved in inflammatory response leukocyte migration cellular response to chemical stimulus taxis response to chemical inflammatory response leukocyte chemotaxis cell surface receptor signaling pathway cell surface receptor protein tyrosine phosphatase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway localization cellular localization receptor clustering macromolecule localization intracellular protein localization localization within membrane protein localization to membrane positive regulation of locomotion positive regulation of chemotaxis positive regulation of cell migration positive regulation of cell motility positive regulation of immune system process regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte chemotaxis positive regulation of leukocyte migration regulation of chemotaxis plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis dendrite arborization dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection arborization regulation of myelination myelination axon ensheathment ensheathment of neurons sexual reproduction oogenesis cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation germ cell development integrin-mediated signaling pathway tissue remodeling bone remodeling ossification involved in bone remodeling positive regulation of cell population proliferation response to auditory stimulus response to mechanical stimulus response to abiotic stimulus regulation of hepatocyte proliferation positive regulation of epithelial cell proliferation hepatocyte proliferation positive regulation of hepatocyte proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of stem cell differentiation stem cell differentiation positive regulation of cell differentiation regulation of stem cell differentiation multi-multicellular organism process placenta development maternal process involved in female pregnancy maternal placenta development female pregnancy multi-organism reproductive process decidualization positive regulation of dendrite development regulation of dendrite development positive regulation of nervous system development regulation of gliogenesis positive regulation of gliogenesis gliogenesis positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation positive regulation of cell development regulation of glial cell differentiation positive regulation of glial cell differentiation central nervous system development oligodendrocyte differentiation glial cell differentiation regulation of oligodendrocyte differentiation	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex extracellular region Schaffer collateral - CA1 synapse synapse cell junction membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex extracellular region Schaffer collateral - CA1 synapse synapse cell junction membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system
A	Integrin alpha-M	amyloid-beta binding binding peptide binding protein binding heat shock protein binding opsonin binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity amyloid-beta binding binding peptide binding protein binding heat shock protein binding opsonin binding complement component C3b binding complement binding cation binding ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity cargo receptor activity cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor binding	regulation of biological process regulation of cellular process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process cellular process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of biological process regulation of cellular process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process cellular process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process positive regulation of cellular process membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination response to stimulus response to stress response to ischemia response to ketone response to curcumin response to ether response to chemical response to oxygen-containing compound biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus developmental process multicellular organismal process visual system development pattern specification process nervous system development regionalization multicellular organism development central nervous system development anatomical structure development sensory system development vertebrate eye-specific patterning system development cell adhesion negative regulation of dopamine metabolic process regulation of amine metabolic process negative regulation of metabolic process negative regulation of biological process dopamine metabolic process primary metabolic process catechol-containing compound metabolic process regulation of primary metabolic process amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process negative regulation of cellular process negative regulation of amine metabolic process regulation of catecholamine metabolic process biogenic amine metabolic process regulation of dopamine metabolic process heterotypic cell-cell adhesion cell-cell adhesion regulation of immune effector process neutrophil activation regulation of localization regulation of myeloid leukocyte mediated immunity positive regulation of leukocyte mediated immunity regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity myeloid leukocyte activation neutrophil activation involved in immune response positive regulation of leukocyte degranulation positive regulation of regulated secretory pathway positive regulation of immune response establishment of localization in cell leukocyte mediated immunity regulation of immune system process positive regulation of immune system process immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis regulation of response to stimulus positive regulation of myeloid leukocyte mediated immunity regulation of immune response cellular localization positive regulation of secretion by cell positive regulation of exocytosis leukocyte activation regulation of regulated secretory pathway positive regulation of response to stimulus neutrophil mediated immunity secretion by cell regulation of secretion by cell positive regulation of secretion regulation of neutrophil degranulation leukocyte activation involved in immune response neutrophil degranulation positive regulation of immune effector process regulation of leukocyte degranulation secretion regulation of transport cell activation export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response positive regulation of transport regulation of exocytosis positive regulation of neutrophil degranulation granulocyte activation macrophage activation leukocyte activation involved in inflammatory response microglial cell activation inflammatory response glial cell activation neuroinflammatory response establishment of protein localization regulation of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane intracellular protein localization establishment of protein localization to membrane regulation of establishment of protein localization localization within membrane protein targeting to membrane regulation of cellular localization regulation of protein targeting macromolecule localization positive regulation of protein targeting to membrane receptor-mediated endocytosis cell-matrix adhesion cell-substrate adhesion cellular developmental process ectoderm development cell differentiation ectodermal cell differentiation tissue development cellular component disassembly complement-mediated synapse pruning cell junction organization cell junction disassembly synapse pruning synapse organization cellular response to stimulus immune response-regulating cell surface receptor signaling pathway complement receptor mediated signaling pathway signaling cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway activation of immune response amyloid-beta clearance integrin-mediated signaling pathway microglial cell mediated cytotoxicity positive regulation of leukocyte mediated cytotoxicity regulation of leukocyte mediated cytotoxicity positive regulation of microglial cell mediated cytotoxicity leukocyte mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of microglial cell mediated cytotoxicity cell killing head development forebrain development animal organ development brain development response to mechanical stimulus response to abiotic stimulus response to amine response to nitrogen compound response to amphetamine response to bacterium response to Gram-positive bacterium response to lipid response to estradiol	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule cell periphery cell surface plasma membrane external side of plasma membrane side of membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle tertiary granule membrane tertiary granule protein-containing complex plasma membrane protein complex membrane protein complex integrin complex plasma membrane signaling receptor complex signaling receptor complex protein complex involved in cell adhesion integrin alphaM-beta2 complex membrane microdomain membrane raft plasma membrane raft plasma membrane region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR020089	Pleiotrophin/Midkine, N-terminal domain	Domain
B	IPR037122	Pleiotrophin/Midkine, N-terminal domain superfamily	Homologous Superfamily
B	IPR020092	Pleiotrophin/Midkine heparin-binding growth factor, conserved site	Conserved Site
B	IPR020090	Pleiotrophin/Midkine, C-terminal domain	Domain
B	IPR000762	Midkine heparin-binding growth factor	Family
B	IPR020091	Pleiotrophin/Midkine disulphide-rich domain superfamily	Homologous Superfamily
B	IPR038130	Pleiotrophin/Midkine, C-terminal domain superfamily	Homologous Superfamily
A	IPR013517	FG-GAP repeat	Repeat
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR013649	Integrin alpha, first immunoglubulin-like domain	Domain
A	IPR002035	von Willebrand factor, type A	Domain
A	IPR048285	Integrin alpha, second immunoglobulin-like domain	Domain
A	IPR032695	Integrin domain superfamily	Homologous Superfamily
A	IPR013519	Integrin alpha beta-propellor	Repeat
A	IPR000413	Integrin alpha chain	Family
A	IPR048633	Integrin alpha-X-like, third Ig-like domain	Domain
A	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
A	IPR018184	Integrin alpha chain, C-terminal cytoplasmic region, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P21246	Mammary Neoplasms, Experimental sarcomatoid carcinoma carcinoma malignant colon neoplasm medulloblastoma ovarian cancer Alzheimer disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia attention deficit hyperactivity disorder, inattentive type Sjogren syndrome breast cancer esophageal adenocarcinoma juvenile dermatomyositis lung adenocarcinoma malignant glioma Mammary Neoplasms, Experimental sarcomatoid carcinoma carcinoma malignant colon neoplasm medulloblastoma ovarian cancer Alzheimer disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia attention deficit hyperactivity disorder, inattentive type Sjogren syndrome breast cancer esophageal adenocarcinoma juvenile dermatomyositis lung adenocarcinoma malignant glioma mammary neoplasms, animal nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma psoriasis autism spectrum disorder ulcerative colitis breast carcinoma Crohn disease glioblastoma large cell medulloblastoma lung cancer malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm Barrett esophagus undifferentiated carcinoma endometriosis interstitial cystitis
A	Pharos: P11215	systemic lupus erythematosus acute promyelocytic leukemia systemic lupus erythematosus, susceptibility to, 6 IgA glomerulonephritis allergic contact dermatitis Crohn ileitis systemic sclerosis interstitial cystitis Libman-Sacks Disease lung disease MALT lymphoma arthritic joint disease non-small cell lung carcinoma bipolar disorder pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia systemic lupus erythematosus acute promyelocytic leukemia systemic lupus erythematosus, susceptibility to, 6 IgA glomerulonephritis allergic contact dermatitis Crohn ileitis systemic sclerosis interstitial cystitis Libman-Sacks Disease lung disease MALT lymphoma arthritic joint disease non-small cell lung carcinoma bipolar disorder pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia chronic obstructive pulmonary disease cutaneous lupus erythematosus tuberculosis Graves disease hematologic disease invasive ductal breast carcinoma lung cancer lupus erythematosus adrenal cortex carcinoma medulloblastoma astrocytic tumor osteosarcoma cancer schizophrenia colitis diffuse scleroderma ulcerative colitis Hashimoto thyroiditis large cell medulloblastoma lung carcinoma malignant mesothelioma autoimmune disease ovarian cancer central nervous system lupus subependymal giant cell astrocytoma Duchenne muscular dystrophy head and neck 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.