6LZ4 | pdb_00006lz4

Crystal structure of PMab-1 Fv-clasp fragment 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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	Mst1_SARAH,V-set	e6lz4E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Mst1_SARAH,V-set	ECOD (1.6)
B	Mst1_SARAH,V-set	e6lz4B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Mst1_SARAH,V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

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, E	PMAB-1 VH(S112C)-SARAH CHIMERA,B, E	V-KAPPA	Rattus norvegicus (Norway rat)	IGKV3S101, IGKJ2-101	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202546-0)
A, D	PMAB-1 VH(S112C)-SARAH CHIMERA,B, E	VH	Rattus norvegicus (Norway rat)	IGHV1-2401, IGHJ301	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E	Light Chain	IGKV3	Kappa	map peptide	SAbDab (2025-11-28)
A, D	Heavy Chain	IGHV1	-	map peptide	SAbDab (2025-11-28)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	MAP peptide	protein binding binding signaling receptor binding	regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development heart development epithelium development visceral serous pericardium development tissue development circulatory system development pericardium development negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of epithelial to mesenchymal transition regulation of developmental process cellular developmental process positive regulation of biological process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process positive regulation of cellular process epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation anatomical structure morphogenesis tube morphogenesis tube development regulation of actin filament-based process actin filament-based movement regulation of actin filament-based movement regulation of myofibroblast contraction actin filament-based process myofibroblast contraction actin-mediated cell contraction lymphangiogenesis vasculature development anatomical structure formation involved in morphogenesis lymph vessel morphogenesis lymph vessel development cell population proliferation regulation of cell-substrate adhesion regulation of substrate adhesion-dependent cell spreading substrate adhesion-dependent cell spreading cell-substrate adhesion respiratory tube development lung development respiratory system development prostaglandin metabolic process icosanoid metabolic process fatty acid metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process prostanoid metabolic process small molecule metabolic process metabolic process monocarboxylic acid metabolic process lipid metabolic process cell migration cell motility regulation of body fluid levels response to stimulus homotypic cell-cell adhesion regulation of cell activation positive regulation of cell-cell adhesion cell-cell adhesion response to stress coagulation regulation of cell-cell adhesion regulation of biological quality response to wounding wound healing regulation of homotypic cell-cell adhesion positive regulation of cell adhesion cell activation hemostasis platelet aggregation blood coagulation regulation of platelet activation regulation of platelet aggregation positive regulation of homotypic cell-cell adhesion positive regulation of platelet aggregation platelet activation cellular response to stimulus signaling signal transduction cell communication regulation of cellular component organization cell projection organization plasma membrane bounded cell projection morphogenesis cell morphogenesis regulation of cell morphogenesis cellular component organization cell projection morphogenesis regulation of lamellipodium organization regulation of lamellipodium morphogenesis cellular component organization or biogenesis regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization lamellipodium organization lamellipodium morphogenesis regulation of plasma membrane bounded cell projection organization regulation of cell shape negative regulation of cell population proliferation regulation of cell population proliferation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion small GTPase-mediated signal transduction Rho protein signal transduction intracellular signal transduction intracellular signaling cassette endothelial cell fate commitment endothelial cell differentiation endothelium development epithelial cell fate commitment lymphatic endothelial cell differentiation epithelial cell differentiation lymphatic endothelial cell fate commitment cell fate commitment regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle G1/S transition of mitotic cell cycle cell cycle process mitotic cell cycle phase transition morphogenesis of an epithelium epiboly involved in wound healing morphogenesis of an epithelial sheet tissue morphogenesis epiboly wound healing, spreading of cells lung alveolus development cellular component disassembly extracellular matrix disassembly positive regulation of cellular component organization positive regulation of extracellular matrix organization extracellular matrix organization positive regulation of extracellular matrix disassembly regulation of extracellular matrix organization regulation of extracellular matrix disassembly extracellular structure organization external encapsulating structure organization	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane ruffle leading edge membrane ruffle membrane cell projection membrane intracellular anatomical structure cytoplasm cytosol actin-based cell projection microvillus microvillus membrane anchoring junction cell junction basal part of cell basal plasma membrane basolateral plasma membrane leading edge of lamellipodium membrane microdomain membrane raft lamellipodium membrane membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle tetraspanin-enriched microdomain filopodium membrane filopodium
B, E	PMab-1 VL-SARAH(S37C) Chimera	-	-	-
A, D	PMab-1 VH(S112C)-SARAH Chimera	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR052684	Podoplanin domain-containing protein	Family

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.