4YO0

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA 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	C1-set_1	e4yo0A2	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)
A	V-set_10	e4yo0A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
C	C1-set_1	e4yo0C2	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)
C	V-set_10	e4yo0C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
B	C1-set_1	e4yo0B1	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)
B	V-set_3	e4yo0B2	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	C1-set_1	e4yo0D1	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)
D	V-set_3	e4yo0D2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
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
A, C	NZ-1 Fab, anti-human podoplanin	VH-CH1	Rattus norvegicus (Norway rat)	IGHV5S1401, IGHJ201, IGHG2A*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_LAMBDA	IMGT (202452-0)
B, D	NZ-1 Fab, anti-human podoplanin	L-LAMBDA	Rattus norvegicus (Norway rat)	IGLV3S201, IGLJ301, IGLJ101, IGLC101, IGLC3*01	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-2A_LAMBDA	IMGT (202452-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C	Heavy Chain	IGHV5	-	pa14 peptide	SAbDab (2025-01-03)
B, D	Light Chain	IGLV3	Lambda	pa14 peptide	SAbDab (2025-01-03)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Heavy chain of antigen binding fragment, Fab	-	-	-
B, D	Light chain of antigen binding fragment, Fab	-	-	-
E, F	PA14 peptide	protein binding binding signaling receptor binding chemokine binding cytokine binding protein-folding chaperone binding	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 regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic 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 regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process 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 tissue development epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation 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 circulatory system development anatomical structure morphogenesis anatomical structure formation involved in morphogenesis lymph vessel morphogenesis lymph vessel development cell adhesion regulation of cell-substrate adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion tube development respiratory tube development lung development respiratory system development 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 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 epithelium development endothelial cell differentiation endothelium development epithelial cell fate commitment lymphatic endothelial cell differentiation epithelial cell differentiation lymphatic endothelial cell fate commitment cell fate commitment morphogenesis of an epithelium epiboly involved in wound healing morphogenesis of an epithelial sheet tissue morphogenesis epiboly wound healing, spreading of cells 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane ruffle leading edge membrane ruffle membrane cell projection membrane cytosol actin-based cell projection microvillus microvillus membrane anchoring junction basal part of cell basal plasma membrane basolateral plasma membrane leading edge of lamellipodium membrane microdomain membrane raft lamellipodium membrane cytoplasmic vesicle intracellular vesicle vesicle tetraspanin-enriched microdomain filopodium membrane filopodium

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: Q86YL7	malignant mesothelioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Peritoneal Surface Malignancy subependymal giant cell astrocytoma astrocytic tumor cancer glioblastoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma peritoneal neoplasm pilocytic astrocytoma malignant mesothelioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Peritoneal Surface Malignancy subependymal giant cell astrocytoma astrocytic tumor cancer glioblastoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma peritoneal neoplasm pilocytic astrocytoma ulcerative colitis atypical teratoid rhabdoid tumor cutaneous lupus erythematosus interstitial cystitis lung carcinoma myopathy ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis breast cancer gastric carcinoma lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 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.