4YNY | pdb_00004yny

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d4ynyc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d4ynya_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d4ynyd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d4ynyb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C		e4ynyC1	A: HTH	X: SH3	H: SH3	T: LRR_1+LRR_8+LRR_14	F:	ECOD (20:10:01)
A		e4ynyA1	A: HTH	X: SH3	H: SH3	T: LRR_1+LRR_8+LRR_14	F:	ECOD (20:10:01)
D		e4ynyD1	A: HTH	X: SH3	H: SH3	T: LRR_1+LRR_8+LRR_14	F:	ECOD (20:10:01)
B		e4ynyB1	A: HTH	X: SH3	H: SH3	T: LRR_1+LRR_8+LRR_14	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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)
B	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 (202609-0)
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 (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C	Heavy Chain	IGHV5	-	-	SAbDab (2026-03-13)
B, D	Light Chain	IGLV3	Lambda	-	SAbDab (2026-03-13)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.