6S8V

Structure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy chain ectodomain

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	d6s8va_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	Neutrophil gelatinase-associated lipocalin (NGAL)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6s8vc1	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	Neutrophil gelatinase-associated lipocalin (NGAL)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6s8vc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	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	Lipocalins	8033646	3001332	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lipocalins	8033646	3001332	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8052503	3001528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8052503	3001528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	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	PF00061	e6s8vA1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: PF00061	ECOD (1.6)
C	PF00061	e6s8vC1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: PF00061	ECOD (1.6)
B	F_UNCLASSIFIED	e6s8vB2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00128	e6s8vB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00128	ECOD (1.6)
D	F_UNCLASSIFIED	e6s8vD2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF00128	e6s8vD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00128	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)
C	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
A, C	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
B, D	PF00128	Alpha amylase, catalytic domain (Alpha-amylase)	Alpha amylase, catalytic domain	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, a ...	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.	Domain
B, D	PF16028	Solute carrier family 3 member 2 N-terminus (SLC3A2_N)	Solute carrier family 3 member 2 N-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Neutrophil gelatinase-associated lipocalin	molecular sequestering activity iron ion sequestering activity metal ion sequestering activity binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding organic cyclic compound binding anion binding macrolide binding heterocyclic compound binding molecular sequestering activity iron ion sequestering activity metal ion sequestering activity binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding organic cyclic compound binding anion binding macrolide binding heterocyclic compound binding enterobactin binding identical protein binding protein binding	multicellular organismal process regulation of biological process homeostatic process biological regulation positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process metabolic process multicellular organismal process regulation of biological process homeostatic process biological regulation positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process metabolic process regulation of multicellular organismal process regulation of metabolic process cellular process apoptotic process cell death programmed cell death biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus defense response to bacterium response to bacterium siderophore transport localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport iron coordination entity transport	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen specific granule lumen secretory granule secretory vesicle cytoplasm specific granule
B, D	4F2 cell-surface antigen heavy chain	monoatomic cation transmembrane transporter activity metal cation:monoatomic cation antiporter activity calcium:monoatomic cation antiporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity antiporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity calcium:sodium antiporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity monoatomic cation transmembrane transporter activity metal cation:monoatomic cation antiporter activity calcium:monoatomic cation antiporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity antiporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity calcium:sodium antiporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid binding protein binding exogenous protein binding alanine transmembrane transporter activity L-amino acid transmembrane transporter activity organic cation transmembrane transporter activity carboxylic acid transmembrane transporter activity amino acid transmembrane transporter activity L-alanine transmembrane transporter activity neutral L-amino acid transmembrane transporter activity organic acid transmembrane transporter activity organic anion transmembrane transporter activity aromatic amino acid transmembrane transporter activity cell adhesion molecule binding cadherin binding virus receptor activity protein heterodimerization activity protein dimerization activity neutral L-amino acid secondary active transmembrane transporter activity identical protein binding protein homodimerization activity L-leucine transmembrane transporter activity branched-chain amino acid transmembrane transporter activity	nitrogen compound transport organic anion transport carboxylic acid transport transport organic substance transport neutral amino acid transport establishment of localization amino acid transport organic acid transport localization branched-chain amino acid transport isoleucine transport thyroid hormone transport regulation of hormone levels nitrogen compound transport organic anion transport carboxylic acid transport transport organic substance transport neutral amino acid transport establishment of localization amino acid transport organic acid transport localization branched-chain amino acid transport isoleucine transport thyroid hormone transport regulation of hormone levels biological regulation hormone transport regulation of biological quality methionine transport organic cation transport sulfur amino acid transport sulfur compound transport valine transport biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction aromatic amino acid transport tryptophan transport proline transport tyrosine transport L-amino acid transport carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process phenylalanine transport response to organic substance response to stimulus response to chemical response to dsRNA response to nitrogen compound response to exogenous dsRNA response to organic cyclic compound import into cell carboxylic acid transmembrane transport amino acid transmembrane transport organic acid transmembrane transport L-alanine transmembrane transport import across plasma membrane L-alanine import across plasma membrane alanine transport transmembrane transport L-alanine transport L-alpha-amino acid transmembrane transport cellular process amino acid import across plasma membrane L-leucine transport L-leucine import across plasma membrane monoatomic ion transport monoatomic cation transport calcium ion transport metal ion transport L-histidine transport basic amino acid transport histidine transport	membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery basal part of cell plasma membrane membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane vacuolar membrane intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle lysosomal membrane cytoplasm organelle membrane lysosome somatodendritic compartment cell body cell pole apical pole of neuron neuronal cell body pigment granule intracellular vesicle melanosome cytoplasmic vesicle apical part of cell apical plasma membrane cell surface anchoring junction cell junction nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen synapse amino acid transport complex protein-containing complex plasma membrane protein complex membrane protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR012674	Calycin	Homologous Superfamily
A, C	IPR003087	Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12	Family
A, C	IPR002345	Lipocalin	Family
A, C	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A, C	IPR022272	Lipocalin family conserved site	Conserved Site
B, D	IPR042280	Amino acid transporter heavy chain SLC3A2	Family
B, D	IPR031984	Solute carrier family 3 member 2, N-terminal domain	Domain
B, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
B, D	IPR006047	Glycosyl hydrolase, family 13, catalytic domain	Domain
B, D	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P80188	rheumatoid arthritis beta thalassemia kidney disease adult acute respiratory distress syndrome Inflammation cancer contact dermatitis heart valve disease calcinosis cutaneous lupus erythematosus ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma acute kidney failure ulcerative colitis rheumatoid arthritis beta thalassemia kidney disease adult acute respiratory distress syndrome Inflammation cancer contact dermatitis heart valve disease calcinosis cutaneous lupus erythematosus ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma acute kidney failure ulcerative colitis benign neoplasm lung cancer malignant pancreatic neoplasm chronic renal failure syndrome nasopharyngeal carcinoma non-small cell lung carcinoma cystic fibrosis pancreatic ductal adenocarcinoma pituitary cancer exocrine pancreatic carcinoma schizophrenia head and neck cancer thalassemia minor hepatocellular carcinoma interstitial cystitis lung carcinoma MALT lymphoma Crohn disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm drug-induced liver injury psoriasis gastric cancer sinusitis hepatitis, non-human animal astrocytic tumor hereditary persistence of fetal hemoglobin lung adenocarcinoma malignant mesothelioma chronic obstructive pulmonary disease
B, D	Pharos: P08195	breast cancer Lung Neoplasms polycystic ovary syndrome diabetes mellitus malignant ependymoma tuberculosis lung benign neoplasm

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 R01GM133198.