4IJ3

Oxidoreductase Fragment of Human QSOX1 in Complex with a FAB Fragment from an Anti- Human QSOX1 Antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4ij3b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4ij3c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Thioredoxin	e4ij3A3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin	ECOD (1.6)
A	KOG1731_1st	e4ij3A4	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: KOG1731_1st	ECOD (1.6)
B	C1-set_4	e4ij3B1	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	V-set	e4ij3B2	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)
C	V-set_8	e4ij3C2	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	C1-set_1	e4ij3C1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	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
B	Fab, anti-QSOX1 (quiescin sulfhydryl oxidase 1)	L-KAPPA	Mus musculus (house mouse)	IGKV6-1701, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
C	Fab, anti-QSOX1 (quiescin sulfhydryl oxidase 1)	H-GAMMA-1	Mus musculus (house mouse)	IGHV2-6-701, IGHV2-6-702, IGHJ301, IGHG101, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1, C-DOMAIN CH2, C-DOMAIN CH3	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Light Chain	IGKV6	Kappa	sulfhydryl oxidase 1	SAbDab (2024-04-19)
C	Heavy Chain	IGHV2	-	sulfhydryl oxidase 1	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00085	Thioredoxin (Thioredoxin)	Thioredoxin	Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.	Domain
A	PF18108	QSOX Trx-like domain (QSOX_Trx1)	QSOX Trx-like domain	This domain is found in Quiescin sulfhydryl oxidase (QSOX), an oxidoreductase present in Homo sapiens capable of both generating and transferring disulfide modules within a single polypeptide. The domain is thioredoxin-like, hence referred to as Trx1 ...	This domain is found in Quiescin sulfhydryl oxidase (QSOX), an oxidoreductase present in Homo sapiens capable of both generating and transferring disulfide modules within a single polypeptide. The domain is thioredoxin-like, hence referred to as Trx1 domain. Trx1 domain has a di-cysteine motif (Cys-X-X-Cys) which is related to the redox-active domains of protein disulfide isomerase. The Trx1 domain is responsible for intramolecular disulfide transfer through the di-cysteine motif [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sulfhydryl oxidase 1	FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding isomerase activity intramolecular oxidoreductase activity catalytic activity, acting on a protein intramolecular oxidoreductase activity, transposing S-S bonds FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding isomerase activity intramolecular oxidoreductase activity catalytic activity, acting on a protein intramolecular oxidoreductase activity, transposing S-S bonds catalytic activity protein disulfide isomerase activity oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor protein-disulfide reductase activity flavin-dependent sulfhydryl oxidase activity thiol oxidase activity	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process negative regulation of cellular catabolic process catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy negative regulation of cellular metabolic process cellular catabolic process negative regulation of cellular process process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of catabolic process negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy regulation of cellular catabolic process regulation of metabolic process cellular component biogenesis cellular component organization cellular component assembly extracellular matrix organization cellular component organization or biogenesis extracellular matrix assembly extracellular structure organization external encapsulating structure organization	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure intracellular membrane-bounded organelle intercellular bridge extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure intracellular membrane-bounded organelle intercellular bridge tertiary granule lumen membrane-enclosed lumen intracellular vesicle endomembrane system intracellular organelle lumen tertiary granule organelle lumen cytoplasmic vesicle secretory granule secretory vesicle cytoplasm Golgi apparatus endoplasmic reticulum lumen endoplasmic reticulum Golgi membrane membrane bounding membrane of organelle organelle membrane vesicle lumen cytoplasmic vesicle lumen secretory granule lumen platelet alpha granule platelet alpha granule lumen specific granule lumen specific granule
B	Light chain of FAB fragment	-	-	-
C	Heavy chain of FAB fragment	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR042568	Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain superfamily	Homologous Superfamily
A	IPR017905	ERV/ALR sulfhydryl oxidase domain	Domain
A	IPR036774	ERV/ALR sulfhydryl oxidase domain superfamily	Homologous Superfamily
A	IPR013766	Thioredoxin domain	Domain
A	IPR041269	Sulfhydryl oxidase, Trx-like domain	Domain
A	IPR039798	Sulfhydryl oxidase	Family
A	IPR040986	Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain	Domain
A	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O00391	pancreatic intraductal papillary-mucinous carcinoma Prescription Drug Abuse spina bifida substance dependence atypical teratoid rhabdoid tumor Crohn disease interstitial cystitis lung carcinoma malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor substance abuse ulcerative colitis breast cancer pancreatic intraductal papillary-mucinous carcinoma Prescription Drug Abuse spina bifida substance dependence atypical teratoid rhabdoid tumor Crohn disease interstitial cystitis lung carcinoma malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor substance abuse ulcerative colitis breast cancer invasive ductal breast carcinoma malignant ependymoma medulloblastoma pancreatic ductal adenocarcinoma pilocytic astrocytoma psoriasis substance-related disorder breast fibroadenoma drug dependence glioblastoma large cell medulloblastoma malignant glioma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.