9KKJ | pdb_00009kkj

Structure of Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb

External Resource: Annotation

SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV4	Kappa	nectin-4	SAbDab (2025-12-26)
B [auth H]	Heavy Chain	IGHV4	-	nectin-4	SAbDab (2025-12-26)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth L]	Bulumtatug	LAG3/CD223	Therapeutic SAbDab (2025-12-26)
B [auth H]	Bulumtatug	LAG3/CD223	Therapeutic SAbDab (2025-12-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	9MW2821 mAb Fab Light chain	-	-	-
B [auth H]	9MW2821 mAb Fab Heavy Chain	-	-	-
C [auth A]	Nectin-4	protein binding binding virus receptor activity exogenous protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity identical protein binding	cell adhesion cell-cell adhesion homophilic cell-cell adhesion cellular process heterophilic cell-cell adhesion regulation of immune effector process lymphocyte mediated immunity regulation of cellular process response to stimulus negative regulation of biological process negative regulation of lymphocyte mediated immunity response to biotic stimulus negative regulation of natural killer cell mediated immunity leukocyte mediated immunity cell adhesion cell-cell adhesion homophilic cell-cell adhesion cellular process heterophilic cell-cell adhesion regulation of immune effector process lymphocyte mediated immunity regulation of cellular process response to stimulus negative regulation of biological process negative regulation of lymphocyte mediated immunity response to biotic stimulus negative regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity regulation of biological process regulation of natural killer cell mediated immunity immune response response to other organism regulation of innate immune response negative regulation of immune response negative regulation of immune effector process response to external stimulus leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity regulation of response to stimulus defense response to other organism negative regulation of response to external stimulus negative regulation of defense response natural killer cell mediated cytotoxicity regulation of immune response regulation of cell killing negative regulation of natural killer cell mediated cytotoxicity regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus response to stress regulation of response to stress negative regulation of leukocyte mediated cytotoxicity negative regulation of cellular process innate immune response response to external biotic stimulus negative regulation of cell killing defense response negative regulation of response to stimulus regulation of leukocyte mediated cytotoxicity biological regulation defense response to symbiont regulation of lymphocyte mediated immunity negative regulation of immune system process immune system process negative regulation of leukocyte mediated immunity cell killing negative regulation of innate immune response	cell-cell junction adherens junction cellular anatomical structure anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell-cell junction adherens junction cellular anatomical structure anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR051427	Nectin and Nectin-like	Family
C [auth A]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth A]	IPR003598	Immunoglobulin subtype 2	Domain
C [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth A]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth A]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth A]	IPR033320	Nectin-3/4, second Ig domain	Domain
C [auth A]	IPR013162	CD80-like, immunoglobulin C2-set	Domain
C [auth A]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: Q96NY8	ectodermal dysplasia-syndactyly syndrome 1 ductal breast carcinoma in situ lung adenocarcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm interstitial cystitis Metastatic urothelial carcinoma pancreatic ductal adenocarcinoma spina bifida

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.