6S8V | pdb_00006s8v

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)
B	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lipocalins	8033646	3001332	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lipocalins	8033646	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		e6s8vB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: YscJ_FliF	F:	ECOD (20:10:01)
D		e6s8vD1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: MacB_PCD	F:	ECOD (20:10:01)
A		e6s8vA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: MacB_PCD	F:	ECOD (20:10:01)
C		e6s8vC1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: YscJ_FliF	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)
B	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (utative)
D	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)
D	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (utative)
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
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	4F2 cell-surface antigen heavy chain	protein binding binding virus receptor activity exogenous protein binding RNA binding double-stranded RNA binding nucleic acid binding protein heterodimerization activity protein dimerization activity alanine transmembrane transporter activity L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity L-alanine transmembrane transporter activity neutral L-amino acid transmembrane transporter activity protein binding binding virus receptor activity exogenous protein binding RNA binding double-stranded RNA binding nucleic acid binding protein heterodimerization activity protein dimerization activity alanine transmembrane transporter activity L-amino acid transmembrane transporter activity amino acid transmembrane transporter activity L-alanine transmembrane transporter activity neutral L-amino acid transmembrane transporter activity transporter activity carboxylic acid transmembrane transporter activity transmembrane transporter activity aromatic amino acid transmembrane transporter activity identical protein binding protein homodimerization activity cell adhesion molecule binding cadherin binding L-leucine transmembrane transporter activity branched-chain amino acid transmembrane transporter activity	nitrogen compound transport organic anion transport carboxylic acid transport transport neutral amino acid transport proline transport L-amino acid transport establishment of localization organic cation transport organic acid transport amino acid transport localization branched-chain amino acid transport isoleucine transport nitrogen compound transport organic anion transport carboxylic acid transport transport neutral amino acid transport proline transport L-amino acid transport establishment of localization organic cation transport organic acid transport amino acid transport localization branched-chain amino acid transport isoleucine transport aromatic amino acid transport tyrosine transport carbohydrate metabolic process primary metabolic process metabolic process cellular process phenylalanine 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 thyroid hormone transport regulation of hormone levels biological regulation hormone transport regulation of biological quality response to stimulus response to chemical response to dsRNA response to nitrogen compound response to exogenous dsRNA import into cell carboxylic acid transmembrane transport amino 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 amino acid import across plasma membrane methionine transport sulfur amino acid transport sulfur compound transport L-leucine transport L-leucine import across plasma membrane monoatomic ion transport monoatomic cation transport calcium ion transport metal ion transport valine transport L-histidine transport basic amino acid transport tryptophan transport	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cell periphery cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane basal part of cell basal plasma membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface anchoring junction cell junction basolateral plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen vacuolar membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane lysosome somatodendritic compartment cell body cell pole apical pole of neuron neuronal cell body synapse amino acid transport complex protein-containing complex plasma membrane protein complex membrane protein complex
A, C	Neutrophil gelatinase-associated lipocalin	binding ion binding anion binding macrolide binding heterocyclic compound binding enterobactin binding small molecule binding cation binding transition metal ion binding iron ion binding metal ion binding identical protein binding protein binding molecular sequestering activity binding ion binding anion binding macrolide binding heterocyclic compound binding enterobactin binding small molecule binding cation binding transition metal ion binding iron ion binding metal ion binding identical protein binding protein binding molecular sequestering activity iron ion sequestering activity metal ion sequestering activity enzyme binding protease binding	response to stimulus response to chemical response to xenobiotic stimulus response to light stimulus response to radiation response to abiotic stimulus response to blue light neuron apoptotic process regulation of biological process regulation of cellular process positive regulation of programmed cell death hippocampal neuron apoptotic process regulation of apoptotic process biological regulation response to stimulus response to chemical response to xenobiotic stimulus response to light stimulus response to radiation response to abiotic stimulus response to blue light neuron apoptotic process regulation of biological process regulation of cellular process positive regulation of programmed cell death hippocampal neuron apoptotic process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process regulation of hippocampal neuron apoptotic process positive regulation of hippocampal neuron apoptotic process cellular process apoptotic process programmed cell death positive regulation of neuron apoptotic process regulation of neuron apoptotic process positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to mycotoxin response to toxic substance cellular response to nutrient levels response to nutrient levels biological process involved in interspecies interaction between organisms 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 innate immune response response to external biotic stimulus response to hexose response to monosaccharide response to carbohydrate response to oxygen-containing compound response to fructose response to iron(II) ion response to metal ion response to iron ion cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor defense response to bacterium response to bacterium response to X-ray cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus cellular response to X-ray response to ionizing radiation cellular response to abiotic stimulus signal transduction in absence of ligand cell surface receptor signaling pathway signaling extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway extrinsic apoptotic signaling pathway in absence of ligand signal transduction response to peptide response to interleukin-6 cellular response to interleukin-6 response to cytokine cellular response to cytokine stimulus acute-phase response inflammatory response acute inflammatory response multicellular organismal process regulation of developmental process endothelium development morphogenesis of an endothelium regulation of endothelial tube morphogenesis positive regulation of developmental process multicellular organism development tube morphogenesis positive regulation of morphogenesis of an epithelium anatomical structure development regulation of morphogenesis of an epithelium regulation of multicellular organismal process epithelial tube morphogenesis regulation of anatomical structure morphogenesis developmental process epithelium development positive regulation of endothelial tube morphogenesis tube development morphogenesis of an epithelium endothelial tube morphogenesis tissue development tissue morphogenesis anatomical structure morphogenesis positive regulation of multicellular organismal process response to acid chemical response to kainic acid response to nitrogen compound response to amino acid cellular response to interleukin-1 response to interleukin-1 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 positive regulation of cellular component organization regulation of cellular component organization cell projection organization regulation of cell projection organization cellular component organization positive regulation of cell projection organization cellular component organization or biogenesis regulation of localization positive regulation of cation transmembrane transport iron import into cell positive regulation of iron ion transmembrane transport positive regulation of monoatomic ion transport establishment of localization in cell positive regulation of monoatomic ion transmembrane transport monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of monoatomic ion transport import across plasma membrane iron ion transmembrane transport positive regulation of iron ion import across plasma membrane transmembrane transport regulation of transmembrane transport chemical homeostasis import into cell cellular localization inorganic ion homeostasis homeostatic process monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport monoatomic cation transmembrane transport intracellular iron ion homeostasis regulation of iron ion transmembrane transport intracellular monoatomic cation homeostasis positive regulation of transmembrane transport monoatomic ion homeostasis intracellular chemical homeostasis regulation of metal ion transport regulation of iron ion import across plasma membrane iron ion import across plasma membrane regulation of transport positive regulation of iron ion transport regulation of iron ion transport inorganic cation import across plasma membrane cellular homeostasis positive regulation of transport regulation of cellular localization inorganic ion import across plasma membrane regulation of monoatomic cation transmembrane transport positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration cell motility locomotion cellular response to increased oxygen levels response to increased oxygen levels response to lipid cellular response to lipopolysaccharide cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to lipid response to molecule of bacterial origin behavior system process learning or memory long-term memory nervous system process cognition memory cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to tumor necrosis factor response to tumor necrosis factor adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis short-term memory response to herbicide reactive oxygen species biosynthetic process positive regulation of reactive oxygen species biosynthetic process reactive oxygen species metabolic process regulation of reactive oxygen species biosynthetic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process response to virus negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of biological process negative regulation of apoptotic process negative regulation of hippocampal neuron apoptotic process negative regulation of cellular process cellular response to nitrogen compound cellular response to amyloid-beta response to amyloid-beta	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
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
A, C	IPR022272	Lipocalin family conserved site	Conserved Site
A, C	IPR012674	Calycin	Homologous Superfamily
A, C	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A, C	IPR003087	Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12	Family
A, C	IPR002345	Lipocalin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P08195	breast cancer Lung Neoplasms polycystic ovary syndrome diabetes mellitus malignant ependymoma tuberculosis lung benign neoplasm
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 chronic renal failure syndrome malignant pancreatic neoplasm nasopharyngeal carcinoma cystic fibrosis non-small cell lung carcinoma 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 drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm psoriasis gastric cancer sinusitis hepatitis, non-human animal astrocytic tumor hereditary persistence of fetal hemoglobin lung adenocarcinoma chronic obstructive pulmonary disease malignant mesothelioma

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.