2ZCK | pdb_00002zck

Crystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an activating 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)
D [auth H]	DUF3239	e2zckH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DUF3239	ECOD (v294.1)
C [auth L]	DUF3239	e2zckL1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DUF3239	ECOD (v294.1)
A [auth P]	DUF3239	e2zckP1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DUF3239	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth P]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	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
D [auth H]	8G8F5 Fab	VH-CH1	Mus musculus (house mouse)	IGHV1-7501, IGHV1-8401, IGHJ401, IGHG2A01, IGHG2A*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202613-0)
C [auth L]	8G8F5 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV3-401, IGKJ102, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth H]	Heavy Chain	IGHV1	-	prostate-specific antigen	SAbDab (2026-04-10)
C [auth L]	Light Chain	IGKV3	Kappa	prostate-specific antigen	SAbDab (2026-04-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C [auth L]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A [auth P]	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth H]	monoclonal antibody 8G8F5 Fab	protein-containing complex binding protein binding binding signaling receptor binding immunoglobulin receptor binding Fc-gamma receptor I complex binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process immune response biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus immune system process B cell mediated immunity regulation of immune response activation of immune response biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	protein-containing complex cellular anatomical structure extracellular region extracellular protein-containing complex immunoglobulin complex, circulating immunoglobulin complex IgG immunoglobulin complex
C [auth L]	monoclonal antibody 8G8F5 Fab	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
B [auth S]	KGISSQY	-	-	-
A [auth P]	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	multicellular organismal process system process regulation of systemic arterial blood pressure circulatory system process regulation of blood pressure biological regulation regulation of biological quality blood circulation regulation of developmental process negative regulation of biological process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis multicellular organismal process system process regulation of systemic arterial blood pressure circulatory system process regulation of blood pressure biological regulation regulation of biological quality blood circulation 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 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 regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of immune system process response to other organism immune response response to external stimulus 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 metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic 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 positive regulation of biological process regulation of antibacterial peptide production 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 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 proteolysis primary metabolic process protein metabolic process zymogen activation protein maturation protein processing	cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth H]	IPR050380	Immune Recognition and Response Modulators	Family
D [auth H]	IPR003597	Immunoglobulin C1-set	Domain
D [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth H]	IPR007110	Immunoglobulin-like domain	Domain
D [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
C [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth L]	IPR007110	Immunoglobulin-like domain	Domain
A [auth P]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth P]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth P]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth P]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth P]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A [auth P]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth P]	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 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.