6ITH | pdb_00006ith

Structure of the transmembrane domain of syndecan 2 in micelles

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ion_trans	e6ithA1	A: alpha bundles	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: Ion_trans	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	Syndecan-2	protein binding binding PDZ domain binding protein domain specific binding identical protein binding	regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of developmental process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of developmental process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation dendrite development neuron projection morphogenesis regulation of dendrite morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis regulation of anatomical structure morphogenesis system development developmental process regulation of biological process plasma membrane bounded cell projection organization regulation of cell projection organization biological regulation dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis regulation of dendrite development neuron development cellular process regulation of plasma membrane bounded cell projection organization cell migration cell motility	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum lytic vacuole vacuolar lumen vacuole lysosomal lumen lysosome cell surface cell periphery plasma membrane membrane extracellular matrix external encapsulating structure

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027789	Syndecan/Neurexin domain	Domain
A	IPR030479	Syndecan, conserved site	Conserved Site
A	IPR001050	Syndecan	Family
A	IPR003585	Neurexin/syndecan/glycophorin C	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P34741	medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis ulcerative colitis ABri amyloidosis amyotrophic lateral sclerosis breast cancer Down syndrome Emery-Dreifuss muscular dystrophy invasive ductal breast carcinoma malignant ependymoma nasopharyngeal carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis ulcerative colitis ABri amyloidosis amyotrophic lateral sclerosis breast cancer Down syndrome Emery-Dreifuss muscular dystrophy invasive ductal breast carcinoma malignant ependymoma nasopharyngeal carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Sjogren syndrome ADan amyloidosis atopic eczema cutaneous lupus erythematosus Duchenne muscular dystrophy facioscapulohumeral muscular dystrophy juvenile dermatomyositis malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer tuberculosis adrenal cortex carcinoma atypical teratoid rhabdoid tumor cystic fibrosis ductal breast carcinoma in situ glioblastoma limb-girdle muscular dystrophy

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Transmembrane	Bitopic proteins	Syndecan	Syndecan

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A	PDBTM	Annotated as membrane protein by PDBTM

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.