6QBA

Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold

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
Membrane Protein Annotation: OPM

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6qbab_	All beta proteins	SH3-like barrel	Chromo domain-like	Histone-like proteins from archaea	automated matches	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
A	d6qbaa_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	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)
B	SCOP2B Superfamily	Chromo domain-like	8077309	3000161	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lipocalins	8042583	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	7kD_DNA_binding	e6qbaB1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: 7kD_DNA_binding	ECOD (1.6)
A	Lipocalin_2	e6qbaA1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF02294	7kD DNA-binding domain (7kD_DNA_binding)	7kD DNA-binding domain	This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.	Domain
A	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
B	DNA-binding protein 7a	DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity	-	-
A	Retinol-binding protein 4	vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding alcohol transmembrane transporter activity retinol transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity organic hydroxy compound transmembrane transporter activity vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding retinal binding alcohol transmembrane transporter activity retinol transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity organic hydroxy compound transmembrane transporter activity vitamin transmembrane transporter activity transporter activity transmembrane transporter activity	multicellular organismal process maintenance of gastrointestinal epithelium system process digestion multicellular organismal-level homeostasis epithelial structure maintenance homeostatic process digestive system process anatomical structure homeostasis tissue homeostasis developmental process heart development multicellular organism development anatomical structure development multicellular organismal process maintenance of gastrointestinal epithelium system process digestion multicellular organismal-level homeostasis epithelial structure maintenance homeostatic process digestive system process anatomical structure homeostasis tissue homeostasis developmental process heart development multicellular organism development anatomical structure development animal organ development circulatory system development system development camera-type eye morphogenesis sensory organ development eye development embryonic morphogenesis visual system development retina development in camera-type eye embryo development retina morphogenesis in camera-type eye anatomical structure morphogenesis eye morphogenesis embryonic retina morphogenesis in camera-type eye sensory organ morphogenesis camera-type eye development animal organ morphogenesis sensory system development urinary bladder development renal system development genitalia development reproductive system development reproductive process female genitalia development sex differentiation female sex differentiation developmental process involved in reproduction vagina development reproductive structure development embryonic organ morphogenesis embryonic organ development tube development respiratory tube development lung development respiratory system development genitalia morphogenesis female genitalia morphogenesis regulation of growth regulation of cellular process regulation of cardiac muscle tissue growth regulation of developmental process developmental growth cardiac muscle cell proliferation negative regulation of biological process negative regulation of cardiac muscle tissue growth organ growth striated muscle tissue development negative regulation of organ growth negative regulation of growth regulation of organ growth regulation of heart growth negative regulation of cellular process regulation of cardiac muscle cell proliferation muscle cell proliferation regulation of multicellular organismal process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation negative regulation of cell population proliferation regulation of biological process heart growth regulation of multicellular organismal development cell population proliferation regulation of developmental growth negative regulation of heart growth cardiac muscle tissue development negative regulation of developmental process biological regulation growth tissue development negative regulation of developmental growth regulation of cell population proliferation cellular process negative regulation of multicellular organismal process negative regulation of cardiac muscle cell proliferation response to retinoic acid response to lipid response to stimulus response to chemical response to oxygen-containing compound cardiac chamber morphogenesis heart trabecula formation heart morphogenesis anatomical structure formation involved in morphogenesis cardiac chamber development heart trabecula morphogenesis trabecula formation trabecula morphogenesis uterus development regulation of immune effector process immunoglobulin production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of immune effector process regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of immune system process positive regulation of cellular process positive regulation of immunoglobulin production regulation of biosynthetic process production of molecular mediator of immune response regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression biosynthetic process regulation of immunoglobulin production positive regulation of gene expression immune system process positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process metabolic process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic process embryo development ending in birth or egg hatching skeletal system development chordate embryonic development embryonic skeletal system development monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process primary metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process small molecule metabolic process glucose metabolic process sensory perception of light stimulus sensory perception nervous system process visual perception localization transport macromolecule localization lipid localization lipid transport organic hydroxy compound transport establishment of localization terpenoid transport isoprenoid transport retinol transport protein localization positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization cell communication cellular macromolecule localization positive regulation of insulin secretion regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion positive regulation of protein localization cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion signaling positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion regulation of signaling secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion hormone transport regulation of cell communication insulin secretion positive regulation of signaling chemical homeostasis glucose homeostasis carbohydrate homeostasis diterpenoid metabolic process organic hydroxy compound metabolic process alcohol metabolic process hormone metabolic process retinoid metabolic process olefinic compound metabolic process retinol metabolic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process primary alcohol metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
B	IPR003212	DNA-binding protein 7a-e	Family
A	IPR012674	Calycin	Homologous Superfamily
A	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A	IPR022272	Lipocalin family conserved site	Conserved Site
A	IPR022271	Lipocalin, ApoD type	Family
A	IPR002449	Retinol binding protein/Purpurin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P02753	microphthalmia, isolated, with coloboma 10 progressive retinal dystrophy due to retinol transport defect keratomalacia vitamin A deficiency polycystic ovary syndrome Necrosis sarcomatoid carcinoma microphthalmia congestive heart failure kidney disease alcoholic liver diseases carcinoma gastric cancer oligodendroglioma pilocytic astrocytoma microphthalmia, isolated, with coloboma 10 progressive retinal dystrophy due to retinol transport defect keratomalacia vitamin A deficiency polycystic ovary syndrome Necrosis sarcomatoid carcinoma microphthalmia congestive heart failure kidney disease alcoholic liver diseases carcinoma gastric cancer oligodendroglioma pilocytic astrocytoma hereditary diffuse gastric adenocarcinoma invasive ductal breast carcinoma psoriasis adrenal cortex adenoma lung carcinoma atopic eczema malignant mesothelioma undifferentiated carcinoma breast carcinoma mammary neoplasms, animal ductal breast carcinoma in situ non-small cell lung carcinoma gastric neoplasm ovarian cancer heart failure pituitary cancer inborn carbohydrate metabolic disorder primitive neuroectodermal tumor adrenal cortex carcinoma lung adenocarcinoma malignant ependymoma type 2 diabetes mellitus atypical teratoid rhabdoid tumor breast fibroadenoma coloboma cystic fibrosis myopathy Emery-Dreifuss muscular dystrophy obesity disorder glioblastoma Pick disease interstitial cystitis adenoma sarcoidosis lung cancer Sjogren syndrome astrocytic tumor malignant glioma ulcerative colitis breast cancer medulloblastoma microphthalmia with coloboma 1

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Monotopic/peripheral	All beta monotopic/peripheral	Calycin	Retinol binding protein-like (n=8,S=12)

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.