5JJD | pdb_00005jjd

crystal structure of the ceramide transfer protein PH and START domain complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5jjda_	All beta proteins	PH domain-like barrel	PH domain-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PH domain-like	8081067	3000134	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)
A	AMP-binding	e5jjdA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: RelE-like	T: RelE-like	F: AMP-binding	ECOD (v294.1)
B	AMP-binding	e5jjdB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: RelE-like	T: RelE-like	F: AMP-binding	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
B	3.30.530.20	Alpha Beta	2-Layer Sandwich	Alpha-D-Glucose-1,6-Bisphosphate	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00169	PH domain (PH)	PH domain	PH stands for pleckstrin homology.	Domain
B	PF01852	START domain (START)	START domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Collagen type IV alpha-3-binding protein	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups phospholipid transfer activity lipid transporter activity lipid transfer activity sphingolipid transfer activity sphingolipid transporter activity transporter activity ceramide transfer activity ceramide 1-phosphate transfer activity phospholipid transporter activity ceramide binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups phospholipid transfer activity lipid transporter activity lipid transfer activity sphingolipid transfer activity sphingolipid transporter activity transporter activity ceramide transfer activity ceramide 1-phosphate transfer activity phospholipid transporter activity ceramide binding binding sphingolipid binding lipid binding ion binding anion binding phospholipid binding ceramide 1-phosphate binding small molecule binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol binding identical protein binding protein binding	membrane organization nitrogen compound transport intermembrane lipid transfer transport lipid localization lipid transport establishment of localization intermembrane sphingolipid transfer cellular component organization localization macromolecule localization cellular process cellular component organization or biogenesis response to stimulus membrane organization nitrogen compound transport intermembrane lipid transfer transport lipid localization lipid transport establishment of localization intermembrane sphingolipid transfer cellular component organization localization macromolecule localization cellular process cellular component organization or biogenesis response to stimulus immune response immune system process ceramide transport cell population proliferation chemical homeostasis homeostatic process lipid homeostasis sphingolipid biosynthetic process lipid biosynthetic process primary metabolic process sphingolipid metabolic process sphingomyelin biosynthetic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process phosphorus metabolic process sphingomyelin metabolic process lipid metabolic process cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation signal transduction cell communication developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development heart development heart morphogenesis animal organ development circulatory system development anatomical structure morphogenesis animal organ morphogenesis system development organelle organization endoplasmic reticulum organization endomembrane system organization cell morphogenesis system process muscle contraction muscle system process ceramide metabolic process mitochondrion organization cellular localization ER to Golgi ceramide transport intracellular lipid transport intracellular transport establishment of localization in cell cellular response to stress response to stress response to endoplasmic reticulum stress	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane Golgi apparatus endoplasmic reticulum-trans-Golgi network membrane contact site organelle membrane contact site
B	Collagen type IV alpha-3-binding protein	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups phospholipid transfer activity lipid transporter activity lipid transfer activity sphingolipid transfer activity sphingolipid transporter activity transporter activity ceramide transfer activity ceramide 1-phosphate transfer activity phospholipid transporter activity ceramide binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups phospholipid transfer activity lipid transporter activity lipid transfer activity sphingolipid transfer activity sphingolipid transporter activity transporter activity ceramide transfer activity ceramide 1-phosphate transfer activity phospholipid transporter activity ceramide binding binding sphingolipid binding lipid binding ion binding anion binding phospholipid binding ceramide 1-phosphate binding small molecule binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol binding identical protein binding protein binding	membrane organization nitrogen compound transport intermembrane lipid transfer transport lipid localization lipid transport establishment of localization intermembrane sphingolipid transfer cellular component organization localization macromolecule localization cellular process cellular component organization or biogenesis response to stimulus membrane organization nitrogen compound transport intermembrane lipid transfer transport lipid localization lipid transport establishment of localization intermembrane sphingolipid transfer cellular component organization localization macromolecule localization cellular process cellular component organization or biogenesis response to stimulus immune response immune system process ceramide transport cell population proliferation chemical homeostasis homeostatic process lipid homeostasis sphingolipid biosynthetic process lipid biosynthetic process primary metabolic process sphingolipid metabolic process sphingomyelin biosynthetic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process phosphorus metabolic process sphingomyelin metabolic process lipid metabolic process cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation signal transduction cell communication developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development heart development heart morphogenesis animal organ development circulatory system development anatomical structure morphogenesis animal organ morphogenesis system development organelle organization endoplasmic reticulum organization endomembrane system organization cell morphogenesis system process muscle contraction muscle system process ceramide metabolic process mitochondrion organization cellular localization ER to Golgi ceramide transport intracellular lipid transport intracellular transport establishment of localization in cell cellular response to stress response to stress response to endoplasmic reticulum stress	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane Golgi apparatus endoplasmic reticulum-trans-Golgi network membrane contact site organelle membrane contact site

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001849	Pleckstrin homology domain	Domain
A	IPR023393	START-like domain superfamily	Homologous Superfamily
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR041952	STARD11, START domain	Domain
A	IPR051213	START domain-containing lipid transfer	Family
A	IPR002913	START domain	Domain
B	IPR001849	Pleckstrin homology domain	Domain
B	IPR023393	START-like domain superfamily	Homologous Superfamily
B	IPR011993	PH-like domain superfamily	Homologous Superfamily
B	IPR041952	STARD11, START domain	Domain
B	IPR051213	START domain-containing lipid transfer	Family
B	IPR002913	START domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y5P4	intellectual disability, autosomal dominant 34 non-small cell lung carcinoma intellectual disability Neurodevelopmental Disorders rheumatoid arthritis adrenal cortex carcinoma glioblastoma invasive ductal breast carcinoma malignant ependymoma pancreatic ductal adenocarcinoma spina bifida atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma myopathy intellectual disability, autosomal dominant 34 non-small cell lung carcinoma intellectual disability Neurodevelopmental Disorders rheumatoid arthritis adrenal cortex carcinoma glioblastoma invasive ductal breast carcinoma malignant ependymoma pancreatic ductal adenocarcinoma spina bifida atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma myopathy osteosarcoma psoriasis epilepsy lung cancer medulloblastoma ovarian cancer
B	Pharos: Q9Y5P4	intellectual disability, autosomal dominant 34 non-small cell lung carcinoma intellectual disability Neurodevelopmental Disorders rheumatoid arthritis adrenal cortex carcinoma glioblastoma invasive ductal breast carcinoma malignant ependymoma pancreatic ductal adenocarcinoma spina bifida atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma myopathy intellectual disability, autosomal dominant 34 non-small cell lung carcinoma intellectual disability Neurodevelopmental Disorders rheumatoid arthritis adrenal cortex carcinoma glioblastoma invasive ductal breast carcinoma malignant ependymoma pancreatic ductal adenocarcinoma spina bifida atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma myopathy osteosarcoma psoriasis epilepsy lung cancer medulloblastoma ovarian 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.