2HKA | pdb_00002hka

Crystal structure of bovine NPC2 and cholesterol sulfate 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2hkab_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	ML domain	Epididymal secretory protein E1 (Niemann-Pick C2 protein)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d2hkac_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	ML domain	Epididymal secretory protein E1 (Niemann-Pick C2 protein)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d2hkaa_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	ML domain	Epididymal secretory protein E1 (Niemann-Pick C2 protein)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	E set domains	8055007	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8055007	3000070	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E set domains	8055007	3000070	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	Copper-bind	e2hkaB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
C	Copper-bind	e2hkaC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
A	Copper-bind	e2hkaA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.770	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	2.60.40.770	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.40.770	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02221	ML domain (E1_DerP2_DerF2)	ML domain	ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2 (Swiss:P49278). It has been implicate in lipid recognition, particularly in the recognition of pa ...	ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2 (Swiss:P49278). It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 (Swiss:Q15668) causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Epididymal secretory protein E1	sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding	localization transport macromolecule localization lipid localization cholesterol transport lipid transport sterol transport organic hydroxy compound transport establishment of localization cellular localization intracellular lipid transport intracellular cholesterol transport intracellular transport intracellular sterol transport localization transport macromolecule localization lipid localization cholesterol transport lipid transport sterol transport organic hydroxy compound transport establishment of localization cellular localization intracellular lipid transport intracellular cholesterol transport intracellular transport intracellular sterol transport establishment of localization in cell cellular process secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process small molecule metabolic process metabolic process primary metabolic process lipid metabolic process cholesterol efflux	cellular anatomical structure extracellular region membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle lysosome endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C	IPR039670	Sterol transport protein NPC2-like	Family
A, B, C	IPR003172	MD-2-related lipid-recognition domain	Domain
A, B, C	IPR033916	Npc2 like, ML domain	Domain

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.