6A0Z | pdb_00006a0z

Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, HA head region


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth L]C1-set_4e6a0zL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
C [auth L]V-sete6a0zL2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
B [auth H]V-set_8e6a0zH2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
B [auth H]C1-set_1e6a0zH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
AHemagglutinin_1ste6a0zA1 A: beta sandwichesX: jelly-rollH: Viral protein domain (From Topology)T: Viral protein domainF: Hemagglutinin_1stECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
C [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
B [auth H]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (utative)
A3.90.209.20 Alpha Beta Alpha-Beta Complex Hemagglutinin (Ha1 Chain) Chain: ACATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
C [auth L]Fab 13D4, broadly neutralizing antibody L-KAPPA Mus musculus (house mouse) IGKV6-15*01, IGKJ5*01, IGKC*01, IGKC*02 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-2A_KAPPA IMGT (202540-0)
B [auth H]Fab 13D4, broadly neutralizing antibody H-GAMMA-2A Mus musculus (house mouse) IGHV1-9*01, IGHJ1*01, IGHJ1*02, IGHG2A*01, IGHG2A*02 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-2A_KAPPA IMGT (202540-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
C [auth L]Light ChainIGKV6 Kappahemagglutinin,envelope glycoproteinSAbDab (2025-10-17)
B [auth H]Heavy ChainIGHV1 -hemagglutinin,envelope glycoproteinSAbDab (2025-10-17)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C [auth L]Antibody 13D4, Fab Light Chain---
B [auth H]Antibody 13D4, Fab Heavy Chain---
Hemagglutinin,Envelope glycoprotein

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
B [auth H]PCA Parent Component: GLN

RESIDAA0031

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