3CZH

Crystal structure of CYP2R1 in complex with vitamin D2

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)
A	d3czha1	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	Vitamin D 25-hydroxylase Cyp2R1	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3czha2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3czhb1	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	Vitamin D 25-hydroxylase Cyp2R1	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3czhb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(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	SCOP2 Family	Cytochrome P450	8027972	4001206	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome P450	8040351	3001061	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cytochrome P450	8040351	3001061	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	p450	e3czhA1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)
B	p450	e3czhB1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
B	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00067	Cytochrome P450 (p450)	Cytochrome P450	Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, a ...	Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cytochrome P450 2R1	vitamin binding binding D3 vitamins binding organic cyclic compound binding vitamin D binding steroid binding lipid binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity tetrapyrrole binding heme binding vitamin binding binding D3 vitamins binding organic cyclic compound binding vitamin D binding steroid binding lipid binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding monooxygenase activity oxidoreductase activity vitamin D3 25-hydroxylase activity vitamin D 25-hydroxylase activity catalytic activity steroid hydroxylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	response to cesium ion response to stimulus response to metal ion response to chemical response to ionizing radiation response to radiation response to abiotic stimulus small molecule metabolic process metabolic process vitamin metabolic process cellular response to stimulus cellular response to chemical stimulus cellular response to xenobiotic stimulus cellular metabolic process response to cesium ion response to stimulus response to metal ion response to chemical response to ionizing radiation response to radiation response to abiotic stimulus small molecule metabolic process metabolic process vitamin metabolic process cellular response to stimulus cellular response to chemical stimulus cellular response to xenobiotic stimulus cellular metabolic process cellular process xenobiotic metabolic process response to xenobiotic stimulus fat-soluble vitamin metabolic process steroid metabolic process organic hydroxy compound metabolic process primary metabolic process vitamin D metabolic process lipid metabolic process cellular biosynthetic process vitamin biosynthetic process lipid biosynthetic process alcohol metabolic process vitamin D3 metabolic process vitamin D biosynthetic process polyol biosynthetic process steroid biosynthetic process polyol metabolic process calcitriol biosynthetic process from calciol small molecule biosynthetic process secondary alcohol metabolic process biosynthetic process organic hydroxy compound biosynthetic process alcohol biosynthetic process fat-soluble vitamin biosynthetic process organic acid metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cellular anatomical entity cytoplasm organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cellular anatomical entity cytoplasm organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002401	Cytochrome P450, E-class, group I	Family
A, B	IPR017972	Cytochrome P450, conserved site	Conserved Site
A, B	IPR050182	Cytochrome P450 family 2	Family
A, B	IPR001128	Cytochrome P450	Family
A, B	IPR036396	Cytochrome P450 superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q6VVX0	vitamin D hydroxylation-deficient rickets, type 1B cirrhosis of liver Vitamin D-dependent rickets vitamin D-dependent rickets, type 1A medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia X-linked dominant hypophosphatemic rickets ovarian cancer Pick disease pancreatic intraductal papillary-mucinous carcinoma rickets

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM				Cytochrome P450

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.