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 4YNY | pdb_00004yny

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

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Dd4ynyd1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)
Bd4ynyb1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)
Cd4ynyc_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) automated matches (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)
Ad4ynya_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) automated matches (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DLRR_1+LRR_8+LRR_14e4ynyD1 A: alpha arraysX: Repetitive alpha hairpinsH: ARM repeatT: ARM repeatF: LRR_1+LRR_8+LRR_14ECOD (v295.2)
BLRR_1+LRR_8+LRR_14e4ynyB1 A: alpha arraysX: Repetitive alpha hairpinsH: ARM repeatT: ARM repeatF: LRR_1+LRR_8+LRR_14ECOD (v295.2)
CLRR_1+LRR_8+LRR_14e4ynyC1 A: alpha arraysX: Repetitive alpha hairpinsH: ARM repeatT: ARM repeatF: LRR_1+LRR_8+LRR_14ECOD (v295.2)
ALRR_1+LRR_8+LRR_14e4ynyA1 A: alpha arraysX: Repetitive alpha hairpinsH: ARM repeatT: ARM repeatF: LRR_1+LRR_8+LRR_14ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
D2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
B2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
C2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
A2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
B, D
NZ-1 Fab, anti-human podoplanin L-LAMBDA Rattus norvegicus (Norway rat) IGLV3S2*01, IGLJ3*01, IGLJ1*01, IGLC1*01, IGLC3*01 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-2A_LAMBDA IMGT (202636-0)
A, C
NZ-1 Fab, anti-human podoplanin VH-CH1 Rattus norvegicus (Norway rat) IGHV5S14*01, IGHJ2*01, IGHG2A*01 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-2A_LAMBDA IMGT (202636-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
B, D
Light ChainIGLV3 Lambda-SAbDab (2026-09-18)
A, C
Heavy ChainIGHV5 --SAbDab (2026-09-18)

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
B, D
PCA Parent Component: GLN

:  AA0031

:  2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420