5DK3 | pdb_00005dk3

Crystal Structure of Pembrolizumab, a full length IgG4 antibody


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AHATPase_ce5dk3A1 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: HATPase_cECOD (develop294)
C [auth F]HATPase_ce5dk3F1 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: HATPase_cECOD (develop294)
BHATPase_ce5dk3B1 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: HATPase_cECOD (develop294)
BEF-hand_1, EF-hand_6, EF-hand_7e5dk3B4 A: alpha bundlesX: Lipocalins/StreptavidinH: SAM/DNA-glycosylaseT: SAM domain-likeF: EF-hand_1, EF-hand_6, EF-hand_7ECOD (develop294)
D [auth G]HATPase_ce5dk3G2 A: alpha bundlesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: HATPase_cECOD (develop294)
D [auth G]EF-hand_1, EF-hand_6, EF-hand_7e5dk3G5 A: alpha bundlesX: Lipocalins/StreptavidinH: SAM/DNA-glycosylaseT: SAM domain-likeF: EF-hand_1, EF-hand_6, EF-hand_7ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
C [auth F]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
B2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (utative)
D [auth G]2.60.40.10 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,
C [auth F]
INN name L-KAPPA Homo sapiens (human) IGKV3D-11*01, IGKJ4*01, IGKJ4*02, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG IG-GAMMA-4_KAPPA IMGT (202610-0)
B,
D [auth G]
INN name H-GAMMA-4 Homo sapiens (human) IGHV1-2*02, IGHJ6*01, IGHJ6*02, IGHG4*01, IGHG4*04 V-DOMAIN VH, C-DOMAIN CH1, C-DOMAIN CH2, C-DOMAIN CH3 IG IG-GAMMA-4_KAPPA IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
A,
C [auth F]
Light ChainIGKV3 Kappa-SAbDab (2026-03-20)
B,
D [auth G]
Heavy ChainIGHV1 --SAbDab (2026-03-20)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

ChainNameTargetProvenance Source
A,
C [auth F]
Pembrolizumab PDCD1/CD279/PD1Therapeutic SAbDab (2026-03-20)
B,
D [auth G]
Pembrolizumab PDCD1/CD279/PD1Therapeutic SAbDab (2026-03-20)