3QUM

Crystal structure of human prostate specific antigen (PSA) in Fab sandwich with a high affinity and a PCa selective antibody

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth P]	PF00089	e3qumP1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: PF00089	ECOD (1.6)
F [auth Q]	PF00089	e3qumQ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: PF00089	ECOD (1.6)
B [auth L]	PF07654	e3qumL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth L]	PF07686	e3qumL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
G [auth M]	PF07654	e3qumM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G [auth M]	PF07686	e3qumM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth H]	PF07654	e3qumH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth H]	PF07686	e3qumH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth K]	PF07654	e3qumK2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
H [auth K]	PF07686	e3qumK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth A]	PF07654	e3qumA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth A]	PF07686	e3qumA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth C]	PF07654	e3qumC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
I [auth C]	PF07686	e3qumC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth B]	PF07654	e3qumB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth B]	PF07686	e3qumB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J [auth D]	PF07654	e3qumD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
J [auth D]	PF07686	e3qumD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth P]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
F [auth Q]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth M]	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)
H [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth D]	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 [auth L], G [auth M]	FAB 5D3D11	L-KAPPA	Mus musculus (house mouse)	IGKV2-13701, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)
C [auth H], H [auth K]	FAB 5D3D11	VH-CH1	Mus musculus (house mouse)	IGHV1-8201, IGHJ202, IGHJ203, IGHG2A01, IGHG2A*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)
D [auth A], I [auth C]	FAB 5D5A5	L-KAPPA	Mus musculus (house mouse)	IGKV3-501, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)
E [auth B], J [auth D]	FAB 5D5A5	VH-CH1	Mus musculus (house mouse)	IGHV1-701, IGHV1-402, IGHV1-401, IGHJ101, IGHJ102, IGHG2A01, IGHG2A*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], G [auth M]	Light Chain	IGKV2	Kappa	prostate-specific antigen	SAbDab (2024-04-26)
C [auth H], H [auth K]	Heavy Chain	IGHV1	-	prostate-specific antigen	SAbDab (2024-04-26)
D [auth A], I [auth C]	Light Chain	IGKV3	Kappa	prostate-specific antigen	SAbDab (2024-04-26)
E [auth B], J [auth D]	Heavy Chain	IGHV1	-	prostate-specific antigen	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth P], F [auth Q]	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P], F [auth Q]	Prostate-specific antigen	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds peptidase activity catalytic activity, acting on a protein endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity	organic substance metabolic process organonitrogen compound metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process regulation of developmental process negative regulation of biological process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development organic substance metabolic process organonitrogen compound metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process regulation of developmental process negative regulation of biological process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of biological process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis biological regulation vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process regulation of humoral immune response antibacterial peptide production regulation of immune effector process positive regulation of response to biotic stimulus regulation of cellular process response to stimulus positive regulation of macromolecule biosynthetic process response to biotic stimulus positive regulation of metabolic process antimicrobial humoral immune response mediated by antimicrobial peptide positive regulation of immune response response to bacterium organic substance biosynthetic process regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of immune system process response to other organism immune response cellular metabolic process response to external stimulus regulation of cellular metabolic process immune effector process regulation of gene expression biosynthetic process regulation of response to stimulus defense response to other organism positive regulation of defense response positive regulation of production of molecular mediator of immune response regulation of immune response regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response regulation of metabolic process regulation of defense response humoral immune response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus cellular biosynthetic process positive regulation of biological process regulation of antibacterial peptide production positive regulation of cellular metabolic process antimicrobial humoral response positive regulation of response to stimulus defense response to bacterium positive regulation of defense response to bacterium positive regulation of antimicrobial peptide production positive regulation of humoral immune response positive regulation of response to external stimulus positive regulation of biosynthetic process antimicrobial peptide production response to stress regulation of response to stress positive regulation of immune effector process response to external biotic stimulus positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process regulation of defense response to bacterium regulation of antimicrobial humoral response defense response defense response to symbiont antibacterial humoral response regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of antimicrobial humoral response regulation of antimicrobial peptide production positive regulation of gene expression immune system process positive regulation of antibacterial peptide production cellular process positive regulation of cellular biosynthetic process proteolysis	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle secretory granule secretory vesicle cytoplasm protein-containing complex nucleus
B [auth L], G [auth M]	Fab 5D3D11 Light Chain	-	-	-
C [auth H], H [auth K]	Fab 5D3D11 Heavy Chain	-	-	-
D [auth A], I [auth C]	Fab 5D5A5 Light Chain	-	-	-
E [auth B], J [auth D]	Fab 5D5A5 Heavy Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth P], F [auth Q]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth P], F [auth Q]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth P], F [auth Q]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth P], F [auth Q]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth P], F [auth Q]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A [auth P], F [auth Q]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth P], F [auth Q]	Pharos: P07288	prostate cancer benign prostatic hyperplasia malignant prostate phyllodes tumor Neoplasm Recurrence, Local prostatic adenoma prostatitis urethral stricture prostate carcinoma carcinoma erectile dysfunction psoriasis

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.