3U9P | pdb_00003u9p

Crystal Structure of Murine Siderocalin in Complex with an Fab Fragment

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
F [auth M]	d3u9pm1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E [auth L]	d3u9pl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth H]	d3u9ph_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D [auth K]	d3u9pk_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A [auth C]	d3u9pc_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth D]	d3u9pd_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2 Family	Retinol binding protein-like	8070907	4002493	SCOP2 (2022-06-29)
A [auth C]	SCOP2 Superfamily	Lipocalins	8070908	3001332	SCOP2 (2022-06-29)
B [auth D]	SCOP2B Superfamily	Lipocalins	8070908	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)
F [auth M]		e3u9pM1	A: EF-hand	X: EF-hand-related	H: EF-hand	T: SH3_1	F:	ECOD (20:10:01)
E [auth L]		e3u9pL1	A: HTH	X: HTH	H: winged helix domain	T: Glutaredoxin	F:	ECOD (20:10:01)
C [auth H]		e3u9pH1	A: HTH	X: HTH	H: winged helix domain	T: Glutaredoxin	F:	ECOD (20:10:01)
D [auth K]		e3u9pK1	A: HTH	X: HTH	H: winged helix domain	T: Glutaredoxin	F:	ECOD (20:10:01)
A [auth C]		e3u9pC1	A: HTH	X: HTH	H: winged helix domain	T: Glutaredoxin	F:	ECOD (20:10:01)
B [auth D]		e3u9pD2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Ank_2, Ank_4, Ank_5	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth C]	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
B [auth D]	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
E [auth L], F [auth M]	Monoclonal Fab Fragment	L-KAPPA	Rattus norvegicus (Norway rat)	IGKV19S201, IGKJ2-301, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202609-0)
C [auth H], D [auth K]	Monoclonal Fab Fragment	VH-CH1	Rattus norvegicus (Norway rat)	IGHV2-101, IGHJ401, IGHG2B*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth L], F [auth M]	Light Chain	IGKV19	Kappa	neutrophil gelatinase-associated lipocalin	SAbDab (2026-03-13)
C [auth H], D [auth K]	Heavy Chain	IGHV2	-	neutrophil gelatinase-associated lipocalin	SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth D]	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
E [auth L], F [auth M]	Monoclonal Fab Fragment Light Chain	-	-	-
C [auth H], D [auth K]	Monoclonal Fab Fragment Heavy Chain	-	-	-
A [auth C], B [auth D]	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 reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process 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 regulation of reactive oxygen species biosynthetic 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol extracellular region extracellular space membrane-bounded organelle vesicle lumen membrane-enclosed lumen intracellular vesicle cytoplasmic vesicle lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol extracellular region extracellular space membrane-bounded organelle vesicle lumen membrane-enclosed lumen intracellular vesicle cytoplasmic vesicle lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle organelle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

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

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.