7CJ2 | pdb_00007cj2

Crystal structure of the Fab antibody complexed with human YKL-40

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
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)
D [auth B]	d7cj2b1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Type II chitinase	Chitinase-3 like protein 1 (GP-39, YKL-40)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d7cj2b2	Alpha and beta proteins (a+b)	FKBP-like	Chitinase insertion domain	Chitinase insertion domain	Chitinase-3 like protein 1 (GP-39, YKL-40)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d7cj2a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Type II chitinase	Chitinase-3 like protein 1 (GP-39, YKL-40)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d7cj2a2	Alpha and beta proteins (a+b)	FKBP-like	Chitinase insertion domain	Chitinase insertion domain	Chitinase-3 like protein 1 (GP-39, YKL-40)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d7cj2l_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth D]	d7cj2d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth K]	d7cj2k_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth C]	d7cj2c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	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)
D [auth B]	SCOP2B Superfamily	(Trans)glycosidases	8044512	3000313	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Chitinase insertion domain	8044513	3000666	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	(Trans)glycosidases	8044512	3000313	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Chitinase insertion domain	8044513	3000666	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	(Trans)glycosidases	8044512	3000313	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	(Trans)glycosidases	8044512	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)
D [auth B]	GH18_chitolectin_chitotriosidase	e7cj2B2	A: a+b two layers	X: FKBP-like	H: Chitinase insertion domain (From Topology)	T: Chitinase insertion domain	F: GH18_chitolectin_chitotriosidase	ECOD (1.6)
D [auth B]	Glyco_hydro_18	e7cj2B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_18	ECOD (1.6)
C [auth A]	GH18_chitolectin_chitotriosidase	e7cj2A2	A: a+b two layers	X: FKBP-like	H: Chitinase insertion domain (From Topology)	T: Chitinase insertion domain	F: GH18_chitolectin_chitotriosidase	ECOD (1.6)
C [auth A]	Glyco_hydro_18	e7cj2A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_18	ECOD (1.6)
F [auth L]	C1-set_4	e7cj2L2	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 L]	V-set	e7cj2L1	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)
B [auth D]	C1-set_4	e7cj2D2	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)
B [auth D]	V-set	e7cj2D1	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)
E [auth K]	C1-set_1	e7cj2K2	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 K]	V-set_12	e7cj2K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
A [auth C]	C1-set_1	e7cj2C2	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)
A [auth C]	V-set_12	e7cj2C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth D], F [auth L]	Light Chain	IGKV1	Kappa	chitinase 3-like 1 (cartilage glycoprotein-39), isoformcra_a	SAbDab (2025-12-26)
A [auth C], E [auth K]	Heavy Chain	IGHV3	-	chitinase 3-like 1 (cartilage glycoprotein-39), isoformcra_a	SAbDab (2025-12-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF00704	Glycosyl hydrolases family 18 (Glyco_hydro_18)	Glycosyl hydrolases family 18		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a	binding carbohydrate binding structural molecule activity extracellular matrix structural constituent chitin binding carbohydrate derivative binding	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling carbohydrate metabolic process primary metabolic process metabolic process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-threonine phosphorylation positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process peptidyl-threonine modification positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process positive regulation of peptidyl-threonine phosphorylation phosphorylation regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process peptidyl-threonine phosphorylation apoptotic process cell death programmed cell death tube development respiratory tube development lung development respiratory system development response to peptide response to chemical response to cytokine response to interleukin-1 regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction response to interleukin-6 positive regulation of interleukin-8 production positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process regulation of biosynthetic process interleukin-8 production gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of interleukin-8 production regulation of catalytic activity regulation of transferase activity activation of NF-kappaB-inducing kinase activity non-canonical NF-kappaB signal transduction regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity positive regulation of molecular function positive regulation of protein kinase activity positive regulation of catalytic activity regulation of protein kinase activity cellular response to tumor necrosis factor cellular response to cytokine stimulus response to tumor necrosis factor response to mechanical stimulus response to abiotic stimulus response to external stimulus regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process chitin metabolic process aminoglycan catabolic process macromolecule catabolic process glucosamine-containing compound catabolic process amino sugar catabolic process aminoglycan metabolic process amino sugar metabolic process chitin catabolic process defense response response to stress inflammatory response	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cell periphery extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cell periphery extracellular matrix external encapsulating structure perinuclear region of cytoplasm vesicle lumen 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 specific granule endoplasmic reticulum
B [auth D], F [auth L]	Fab(Light chain)	-	-	-
A [auth C], E [auth K]	Fab(Heavy chain)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR029070	Chitinase insertion domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR001223	Glycoside hydrolase family 18, catalytic domain	Domain
C [auth A], D [auth B]	IPR011583	Chitinase II/V-like, catalytic domain	Domain
C [auth A], D [auth B]	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR050314	Glycosyl Hydrolase Family 18	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], D [auth B]	Pharos: P36222	schizophrenia malignant glioma glioblastoma asthma-related traits, susceptibility to, 7 mixed glioma Neoplasm Invasiveness giant cell glioblastoma malignant mesothelioma osteoarthritis asthma osteosarcoma chronic obstructive pulmonary disease pilocytic astrocytoma gastric carcinoma pterygium schizophrenia malignant glioma glioblastoma asthma-related traits, susceptibility to, 7 mixed glioma Neoplasm Invasiveness giant cell glioblastoma malignant mesothelioma osteoarthritis asthma osteosarcoma chronic obstructive pulmonary disease pilocytic astrocytoma gastric carcinoma pterygium glioma ulcerative colitis large cell medulloblastoma lung cancer malignant ependymoma MALT lymphoma myopathy non-small cell lung carcinoma osteoarthritis susceptibility 1 ovarian cancer cystic fibrosis pituitary cancer head and neck cancer limb-girdle muscular dystrophy lung carcinoma medulloblastoma nasopharyngeal carcinoma obesity disorder breast cancer pancreatic ductal adenocarcinoma ductal breast carcinoma in situ primitive neuroectodermal tumor sinusitis interstitial cystitis lung adenocarcinoma malignant colon 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 R01GM157729.