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 3I9G | pdb_00003i9g

Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with sphingosine-1-phosphate

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
B [auth L]d3i9gl2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
B [auth L]d3i9gl1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
A [auth H]d3i9gh_ All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
B [auth L]PDEase_Ie3i9gL1 A: alpha arraysX: Alpha-beta plaitsH: Phage tail protein-likeT: Transmembrane protein 14AF: PDEase_IECOD (v295.2)
A [auth H]EVEe3i9gH1 A: alpha arraysX: Spectrin repeat-likeH: Enzyme IIa from lactose specific PTS, IIa-lacT: Enzyme IIa from lactose specific PTS, IIa-lacF: EVEECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
B [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
A [auth H]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
B [auth L]LT1009 L-KAPPA Homo sapiens (human) IGKV17-121*01, IGKJ4*01, IGKJ4*02, IGKC*03 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202637-0)
A [auth H]LT1009 VH-CH1 Homo sapiens (human) IGHV1-78*01, IGHJ4*01, IGHG1*02 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202637-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
B [auth L]Light ChainIGKV1 Kappa(2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YL DIHYDROGEN PHOSPHATESAbDab (2026-09-25)
A [auth H]Heavy ChainIGHV5 -(2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YL DIHYDROGEN PHOSPHATESAbDab (2026-09-25)