3U9P

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)
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)
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)
E [auth L]	d3u9pl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F [auth M]	d3u9pm1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	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)
A [auth C]	Lipocalin	e3u9pC1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin	ECOD (1.6)
B [auth D]	Lipocalin	e3u9pD2	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin	ECOD (1.6)
C [auth H]	V-set_8	e3u9pH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e3u9pH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth K]	V-set_8	e3u9pK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth K]	C1-set_1	e3u9pK2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth L]	C1-set_4	e3u9pL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth L]	V-set	e3u9pL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
F [auth M]	C1-set_4	e3u9pM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
F [auth M]	V-set	e3u9pM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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
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 (202447-0)
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 (202447-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], D [auth K]	Heavy Chain	IGHV2	-	neutrophil gelatinase-associated lipocalin	SAbDab (2024-11-29)
E [auth L], F [auth M]	Light Chain	IGKV19	Kappa	neutrophil gelatinase-associated lipocalin	SAbDab (2024-11-29)

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
A [auth C], B [auth D]	Neutrophil gelatinase-associated lipocalin	molecular sequestering activity iron ion sequestering activity metal ion sequestering activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding anion binding macrolide binding heterocyclic compound binding molecular sequestering activity iron ion sequestering activity metal ion sequestering activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding anion binding macrolide binding heterocyclic compound binding enterobactin binding	cellular response to stimulus regulation of biological process regulation of cellular process signal transduction in absence of ligand response to stimulus cell surface receptor signaling pathway signaling biological regulation cell death extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway extrinsic apoptotic signaling pathway in absence of ligand cellular process cellular response to stimulus regulation of biological process regulation of cellular process signal transduction in absence of ligand response to stimulus cell surface receptor signaling pathway signaling biological regulation cell death extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway extrinsic apoptotic signaling pathway in absence of ligand cellular process signal transduction apoptotic process programmed cell death multicellular organismal process homeostatic process 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 positive regulation of cellular process biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus response to virus immune response defense response defense response to symbiont immune system process defense response to other organism response to stress innate immune response defense 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	membrane-bounded organelle vesicle lumen intracellular anatomical structure membrane-enclosed lumen intracellular vesicle cytoplasmic vesicle lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen cytoplasmic vesicle organelle cytoplasm membrane-bounded organelle vesicle lumen intracellular anatomical structure membrane-enclosed lumen intracellular vesicle cytoplasmic vesicle lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen cytoplasmic vesicle organelle cytoplasm vesicle extracellular region cytosol extracellular space
C [auth H], D [auth K]	Monoclonal Fab Fragment Heavy Chain	-	-	-
E [auth L], F [auth M]	Monoclonal Fab Fragment Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth D]	IPR012674	Calycin	Homologous Superfamily
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
A [auth C], B [auth D]	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A [auth C], B [auth D]	IPR022272	Lipocalin family conserved site	Conserved Site

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.