3BD3 | pdb_00003bd3

Crystal structure of single domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Bd3bd3b_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) automated matches house mouse (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
Ad3bd3a_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) automated matches house mouse (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BMe-amine-dh_He3bd3B1 A: alpha bundlesX: HTHH: NudixT: NudixF: Me-amine-dh_HECOD (develop294)
AMe-amine-dh_He3bd3A1 A: alpha bundlesX: HTHH: NudixT: NudixF: Me-amine-dh_HECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
B2.60.40.10 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
A, B
VL of 3D8 scFv, anti-DNA V-KAPPA Mus musculus (house mouse) IGKV8-21*01, IGKJ2*03 V-DOMAIN V-KAPPA IG (V-KAPPA) IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
A, B
Light ChainIGKV8 Kappa-SAbDab (2026-03-20)