4YKO | pdb_00004yko

Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32Y:F3Q mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.58 angstrom resolution

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)
B	d4ykob_	All beta proteins	Lipocalins	Lipocalins	Fatty acid binding protein-like	Cellular retinoic-acid-binding protein (CRABP)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4ykoa_	All beta proteins	Lipocalins	Lipocalins	Fatty acid binding protein-like	Cellular retinoic-acid-binding protein (CRABP)	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)
B	SCOP2B Superfamily	Lipocalins	8041239	3001332	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lipocalins	8041239	3001332	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		e4ykoB1	A: HTH	X: HTH	H: Putative DNA-binding domain	T: Insulin	F:	ECOD (20:10:01)
A		e4ykoA1	A: HTH	X: HTH	H: Putative DNA-binding domain	T: Insulin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
A	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00061	Lipocalin / cytosolic fatty-acid binding protein family (Lipocalin)	Lipocalin / cytosolic fatty-acid binding protein family	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid ...	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cellular retinoic acid-binding protein 2	vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding small molecule binding fatty acid binding organic acid binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding alcohol binding vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding small molecule binding fatty acid binding organic acid binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding alcohol binding retinol binding protein binding cyclin binding retinoic acid binding	organic anion transport carboxylic acid transport transport lipid localization lipid transport establishment of localization organic acid transport localization monocarboxylic acid transport fatty acid transport macromolecule localization regulation of cellular process RNA metabolic process regulation of primary metabolic process organic anion transport carboxylic acid transport transport lipid localization lipid transport establishment of localization organic acid transport localization monocarboxylic acid transport fatty acid transport macromolecule localization regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process developmental process multicellular organismal process limb development appendage development embryonic forelimb morphogenesis embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development multicellular organism development anatomical structure morphogenesis forelimb morphogenesis appendage morphogenesis anatomical structure development limb morphogenesis diterpenoid metabolic process oxoacid metabolic process regulation of hormone levels carboxylic acid metabolic process organic acid metabolic process hormone metabolic process retinoic acid metabolic process retinoid metabolic process small molecule metabolic process regulation of biological quality monocarboxylic acid metabolic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size cell projection organization developmental growth regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization positive regulation of developmental growth system development positive regulation of collateral sprouting regulation of cell projection organization positive regulation of cell development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of collateral sprouting 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 growth cell morphogenesis cellular component organization regulation of nervous system development neurogenesis regulation of extent of cell growth 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 cellular process regulation of anatomical structure morphogenesis positive regulation of axonogenesis regulation of cell size regulation of multicellular organismal development collateral sprouting regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size epidermis development tissue development cellular response to stimulus response to stimulus signaling signal transduction cell communication	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000463	Cytosolic fatty-acid binding	Domain
A, B	IPR012674	Calycin	Homologous Superfamily
A, B	IPR031259	Intracellular lipid binding protein	Family
A, B	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P29373	methylmalonic acidemia breast carcinoma esophageal adenocarcinoma invasive ductal breast carcinoma malignant mesothelioma non-small cell lung carcinoma pituitary cancer ductal breast carcinoma in situ facioscapulohumeral muscular dystrophy lung adenocarcinoma medulloblastoma osteosarcoma psoriasis endometriosis interstitial cystitis methylmalonic acidemia breast carcinoma esophageal adenocarcinoma invasive ductal breast carcinoma malignant mesothelioma non-small cell lung carcinoma pituitary cancer ductal breast carcinoma in situ facioscapulohumeral muscular dystrophy lung adenocarcinoma medulloblastoma osteosarcoma psoriasis endometriosis interstitial cystitis lung cancer ovarian cancer Recurrence

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.