4GVD

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide

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)
A	PF00595	e4gvdA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PF00595	ECOD (1.6)
B	PF00595	e4gvdB1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PF00595	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain
C, D	PF01034	Syndecan domain (Syndecan)	Syndecan domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	T-lymphoma invasion and metastasis-inducing protein 1	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding protein tyrosine kinase binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding lipid binding GTPase regulator activity enzyme regulator activity cytoskeletal protein binding microtubule binding protein binding binding tubulin binding protein tyrosine kinase binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding lipid binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular process signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway multicellular organismal process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular process signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway multicellular organismal process positive regulation of nervous system development axonogenesis cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization cell migration cell motility Wnt signaling pathway, planar cell polarity pathway non-canonical Wnt signaling pathway Wnt signaling pathway small GTPase-mediated signal transduction Rac protein signal transduction intracellular signal transduction intracellular signaling cassette regulation of signaling regulation of signal transduction regulation of MAPK cascade regulation of intracellular signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade protein localization localization cellular localization cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane regulation of Wnt signaling pathway regulation of non-canonical Wnt signaling pathway regulation of protein binding positive regulation of molecular function regulation of molecular function positive regulation of protein binding regulation of binding positive regulation of binding positive regulation of dendritic spine morphogenesis positive regulation of dendritic spine development regulation of cell morphogenesis regulation of dendrite morphogenesis regulation of synapse structure or activity dendritic spine morphogenesis synapse organization regulation of biological quality dendritic spine development dendritic spine organization postsynapse organization regulation of postsynapse organization positive regulation of cell morphogenesis regulation of dendrite development regulation of dendritic spine development dendrite development positive regulation of neuron projection development dendrite morphogenesis positive regulation of dendrite morphogenesis regulation of synapse organization cell junction organization regulation of dendritic spine morphogenesis neuron projection organization cell adhesion cell-matrix adhesion cell-substrate adhesion cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly dopaminergic neuron differentiation regulation of dopaminergic neuron differentiation regulation of neuron differentiation regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition mesenchyme development animal organ development tissue development epithelial to mesenchymal transition mesenchymal cell differentiation positive regulation of locomotion regulation of cell motility Schwann cell chemotaxis positive regulation of Schwann cell chemotaxis positive regulation of chemotaxis positive regulation of cell migration gliogenesis taxis chemotaxis regulation of Schwann cell chemotaxis response to external stimulus response to chemical regulation of locomotion regulation of response to external stimulus glial cell migration regulation of Schwann cell migration regulation of glial cell migration positive regulation of Schwann cell migration positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration locomotion cell chemotaxis regulation of chemotaxis Schwann cell migration positive regulation of glial cell migration cellular response to chemical stimulus developmental growth cell growth neuron projection extension developmental cell growth growth developmental growth involved in morphogenesis regulation of localization establishment of protein localization response to organic substance nitrogen compound transport carbohydrate homeostasis establishment of localization in cell regulation of peptide hormone secretion regulation of hormone levels organic substance transport establishment of protein localization to extracellular region intracellular glucose homeostasis protein secretion establishment of localization cellular response to oxygen-containing compound regulation of protein secretion regulation of secretion cellular response to carbohydrate stimulus chemical homeostasis response to glucose glucose homeostasis insulin secretion involved in cellular response to glucose stimulus regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport homeostatic process hormone secretion protein localization to extracellular region peptide secretion secretion by cell regulation of secretion by cell response to monosaccharide response to carbohydrate amide transport signal release cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to organic substance secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell response to oxygen-containing compound cellular response to glucose stimulus regulation of protein transport peptide transport response to hexose cellular homeostasis protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport insulin secretion cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation muscle hypertrophy system process cardiac muscle hypertrophy striated muscle hypertrophy muscle system process regulation of small GTPase mediated signal transduction activation of GTPase activity positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity regulation of modification of postsynaptic actin cytoskeleton regulation of modification of synaptic structure modification of postsynaptic actin cytoskeleton regulation of modification of postsynaptic structure modification of synaptic structure modification of postsynaptic structure response to organonitrogen compound response to nitrogen compound response to organic cyclic compound response to cocaine response to alkaloid	extrinsic component of plasma membrane postsynaptic specialization membrane synapse extrinsic component of postsynaptic density membrane postsynaptic density membrane cell periphery cell junction extrinsic component of postsynaptic specialization membrane asymmetric synapse postsynaptic specialization membrane plasma membrane cellular anatomical entity synaptic membrane extrinsic component of plasma membrane postsynaptic specialization membrane synapse extrinsic component of postsynaptic density membrane postsynaptic density membrane cell periphery cell junction extrinsic component of postsynaptic specialization membrane asymmetric synapse postsynaptic specialization membrane plasma membrane cellular anatomical entity synaptic membrane extrinsic component of synaptic membrane postsynapse postsynaptic density neuron to neuron synapse organelle postsynaptic membrane plasma membrane region extrinsic component of membrane extrinsic component of postsynaptic membrane cell-cell junction anchoring junction intracellular anatomical structure cytoplasm cytosol glutamatergic synapse neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree cell body neuronal cell body polymeric cytoskeletal fiber intracellular organelle cytoskeleton intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle growth cone axon distal axon axonal growth cone site of polarized growth ruffle cell leading edge leading edge membrane ruffle membrane cell projection membrane cell-cell contact zone main axon
C, D	Syndecan-1	cargo receptor activity identical protein binding protein binding binding	response to stimulus response to metal ion response to chemical response to calcium ion response to inorganic substance cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling canonical Wnt signaling pathway biological regulation cell communication cellular process response to stimulus response to metal ion response to chemical response to calcium ion response to inorganic substance cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling canonical Wnt signaling pathway biological regulation cell communication cellular process signal transduction Wnt signaling pathway developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development cell development myoblast development myoblast differentiation response to toxic substance cell migration cell motility response to corticosteroid response to organic substance response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid response to organic cyclic compound ureteric bud development multicellular organismal process mesonephric epithelium development epithelium development kidney epithelium development mesonephros development tube development animal organ development tissue development renal system development multicellular organism development kidney development mesonephric tubule development system development exosomal secretion establishment of organelle localization regulation of localization cellular localization transport positive regulation of biological process positive regulation of secretion by cell positive regulation of exosomal secretion vesicle-mediated transport positive regulation of exocytosis cellular component biogenesis localization secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization establishment of localization in cell cellular component organization or biogenesis positive regulation of cellular process vesicle localization positive regulation of cellular component biogenesis secretion regulation of transport regulation of exosomal secretion establishment of vesicle localization export from cell regulation of cellular component biogenesis regulation of vesicle-mediated transport establishment of localization extracellular exosome biogenesis regulation of secretion exocytosis positive regulation of transport extracellular vesicle biogenesis regulation of exocytosis response to organonitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP reproductive process sex differentiation developmental process involved in reproduction epithelial cell differentiation Sertoli cell differentiation male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development gonad development reproductive system development Sertoli cell development epithelial cell development muscle cell differentiation striated muscle cell development muscle cell development striated muscle cell differentiation positive regulation of extracellular exosome assembly positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of extracellular exosome assembly cellular component organization vesicle organization cellular component assembly extracellular exosome assembly organelle assembly regulation of organelle organization organelle organization regulation of organelle assembly positive regulation of organelle assembly response to hydrogen peroxide response to oxidative stress response to stress response to reactive oxygen species import into cell receptor-mediated endocytosis endocytosis	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex Golgi apparatus endomembrane system Golgi lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003116	Raf-like Ras-binding	Domain
A, B	IPR000219	Dbl homology (DH) domain	Domain
A, B	IPR040655	TIAM1, CC-Ex domain	Domain
A, B	IPR035899	Dbl homology (DH) domain superfamily	Homologous Superfamily
A, B	IPR001849	Pleckstrin homology domain	Domain
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR043537	Tiam1/Tiam2/Protein still life	Family
A, B	IPR001331	Guanine-nucleotide dissociation stimulator, CDC24, conserved site	Conserved Site
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR001478	PDZ domain	Domain
C, D	IPR027789	Syndecan/Neurexin domain	Domain
C, D	IPR030479	Syndecan, conserved site	Conserved Site
C, D	IPR001050	Syndecan	Family
C, D	IPR003585	Neurexin/syndecan/glycophorin C	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q13009	squamous cell carcinoma amyotrophic lateral sclerosis type 1 Mouth Neoplasms ovarian cancer primitive neuroectodermal tumor amyotrophic lateral sclerosis common variable immunodeficiency ductal breast carcinoma in situ interstitial cystitis malignant ependymoma nephrosclerosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor squamous cell carcinoma amyotrophic lateral sclerosis type 1 Mouth Neoplasms ovarian cancer primitive neuroectodermal tumor amyotrophic lateral sclerosis common variable immunodeficiency ductal breast carcinoma in situ interstitial cystitis malignant ependymoma nephrosclerosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor cystic fibrosis esophageal adenocarcinoma large cell medulloblastoma malignant glioma medulloblastoma oral cavity neoplasm pituitary cancer Sjogren syndrome colorectal cancer Down syndrome glioblastoma lung cancer malignant mesothelioma
C, D	Pharos: P18827	malignant mesothelioma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ABri amyloidosis spina bifida breast cancer cancer glioblastoma invasive ductal breast carcinoma lung carcinoma malignant glioma medulloblastoma osteosarcoma malignant mesothelioma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ABri amyloidosis spina bifida breast cancer cancer glioblastoma invasive ductal breast carcinoma lung carcinoma malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor ADan amyloidosis breast carcinoma cystic fibrosis hematologic disease large cell medulloblastoma lymphatic system disease nephrosclerosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis atypical teratoid rhabdoid tumor breast fibroadenoma ductal breast carcinoma in situ interstitial cystitis lung adenocarcinoma malignant ependymoma

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 R01GM133198.