8S6V | pdb_00008s6v

Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide

External Resource: Annotation

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

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C	Heavy Chain	IGHV1	-	mucin-1 subunit alpha	SAbDab (2025-12-05)
B, D	Light Chain	IGKV8	Kappa	mucin-1 subunit alpha	SAbDab (2025-12-05)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	G2D11 (VH-CH1)	-	-	-
B, D	2D9 (VL-CL)	-	-	-
E [auth M], F [auth N]	Mucin-1 subunit alpha	p53 binding protein binding binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding p53 binding protein binding binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding	cellular response to stimulus regulation of cellular process response to stimulus negative regulation of biological process regulation of cellular response to stress regulation of signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death intracellular signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator cell communication negative regulation of apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage cellular response to stimulus regulation of cellular process response to stimulus negative regulation of biological process regulation of cellular response to stress regulation of signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death intracellular signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator cell communication negative regulation of apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage signal transduction intrinsic apoptotic signaling pathway negative regulation of signal transduction by p53 class mediator regulation of biological process negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage negative regulation of apoptotic process regulation of response to stimulus intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of intrinsic apoptotic signaling pathway negative regulation of cell communication intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator negative regulation of cellular process regulation of signaling negative regulation of response to stimulus biological regulation signal transduction by p53 class mediator negative regulation of signal transduction apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator DNA damage response regulation of cell communication cellular process apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of transcription by competitive promoter binding negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell adhesion mediated by integrin DNA damage response, signal transduction by p53 class mediator signal transduction in response to DNA damage regulation of cell cycle phase transition DNA damage checkpoint signaling negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm vesicle cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromatin chromosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth M], F [auth N]	IPR036364	SEA domain superfamily	Homologous Superfamily
E [auth M], F [auth N]	IPR000082	SEA domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth M], F [auth N]	Pharos: P15941	tubulointerstitial kidney disease, autosomal dominant, 2 plasma cell myeloma malignant mesothelioma Crohn disease Precancerous Conditions gastric neoplasm spina bifida invasive ductal breast carcinoma lung cancer ulcerative colitis malignant ependymoma atypical teratoid rhabdoid tumor myeloid neoplasm brain aneurysm non-alcoholic fatty liver disease tubulointerstitial kidney disease, autosomal dominant, 2 plasma cell myeloma malignant mesothelioma Crohn disease Precancerous Conditions gastric neoplasm spina bifida invasive ductal breast carcinoma lung cancer ulcerative colitis malignant ependymoma atypical teratoid rhabdoid tumor myeloid neoplasm brain aneurysm non-alcoholic fatty liver disease cancer ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ductal breast carcinoma in situ plasma cell neoplasm gastric adenocarcinoma psoriasis glioblastoma large cell medulloblastoma transitional cell carcinoma lung carcinoma malignant glioma malignant pancreatic neoplasm autosomal dominant medullary cystic kidney disease with or without hyperuricemia nasopharyngeal carcinoma breast carcinoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma congenital anomaly of kidney and urinary tract peritoneal neoplasm dental caries pituitary cancer endometriosis precancerous condition gastric cancer Sjogren syndrome hereditary diffuse gastric adenocarcinoma lung adenocarcinoma lung disease mesothelioma benign mesothelioma breast disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm digestive system disease esophageal adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth M], F [auth N]	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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.