2ZPK

Crystal structure of P20.1 Fab fragment in complex with its antigen peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]	C1-set	e2zpkL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
A [auth L]	V-set_3	e2zpkL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D [auth M]	C1-set	e2zpkM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
D [auth M]	V-set_3	e2zpkM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
B [auth H]	V-set_8	e2zpkH1	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)
B [auth H]	C1-set_1	e2zpkH2	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 I]	V-set_8	e2zpkI1	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)
E [auth I]	C1-set_1	e2zpkI2	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 [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	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
A [auth L], D [auth M]	P20.1	L-LAMBDA	Mus musculus (house mouse)	IGLV101, IGLJ101, IGLC1*01	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202452-0)
B [auth H], E [auth I]	P20.1	VH-CH1	Mus musculus (house mouse)	IGHV9-402, IGHJ301, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202452-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], D [auth M]	Light Chain	IGLV1	Lambda	proteinase-activated receptor 4	SAbDab (2025-01-03)
B [auth H], E [auth I]	Heavy Chain	IGHV9	-	proteinase-activated receptor 4	SAbDab (2025-01-03)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L], D [auth M]	IgG1-lambda P20.1 Fab (light chain)	-	-	-
B [auth H], E [auth I]	IgG1-lambda P20.1 Fab (heavy chain)	-	-	-
C [auth P], F [auth Q]	Proteinase-activated receptor 4	molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity protein binding binding enzyme binding protease binding peptide receptor activity thrombin-activated receptor activity proteinase-activated receptor activity G protein-coupled peptide receptor activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation multicellular organismal process regulation of body fluid levels wound healing response to stimulus cell activation hemostasis biological regulation blood coagulation response to stress coagulation cellular process regulation of biological quality response to wounding platelet activation cellular response to stimulus regulation of biological process regulation of cellular process signaling phospholipase C-activating G protein-coupled receptor signaling pathway cell communication G protein-coupled receptor signaling pathway signal transduction vesicle organization cellular component organization platelet dense granule organization organelle organization secretory granule organization cellular component organization or biogenesis endomembrane system organization regulation of calcium ion transport regulation of localization positive regulation of cation transmembrane transport positive regulation of calcium ion transport intracellular calcium ion homeostasis negative regulation of biological process calcium ion transport localization positive regulation of monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation homeostasis monoatomic cation transport intracellular monoatomic ion homeostasis regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport chemical homeostasis cellular localization inorganic ion homeostasis transport homeostatic process monoatomic ion transmembrane transport positive regulation of biological process calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis negative regulation of cellular process positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport intracellular chemical homeostasis positive regulation of release of sequestered calcium ion into cytosol regulation of metal ion transport regulation of sequestering of calcium ion positive regulation of cellular process calcium ion transmembrane import into cytosol regulation of transport sequestering of calcium ion cellular homeostasis positive regulation of transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction Rho protein signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling homotypic cell-cell adhesion platelet aggregation cell adhesion cell-cell adhesion	cellular anatomical structure extracellular region cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth P], F [auth Q]	IPR003912	Protease-activated receptor	Family
C [auth P], F [auth Q]	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
C [auth P], F [auth Q]	IPR003944	Protease-activated receptor 4	Family
C [auth P], F [auth Q]	IPR017452	GPCR, rhodopsin-like, 7TM	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth P], F [auth Q]	Pharos: Q96RI0	peliosis hepatis cholestasis Chemical and Drug Induced Liver Injury drug-induced liver injury lung adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth L], D [auth M]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420
B [auth H], E [auth I]	PCA	Parent Component: GLN RESID: AA0031 , AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.