6LDY | pdb_00006ldy

Structure antibody D6 in complex with methylated peptide

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	C1-set	e6ldyB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
B	V-set	e6ldyB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth L]	C1-set	e6ldyL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
E [auth L]	V-set	e6ldyL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
A	V-set_8	e6ldyA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	C1-set_1	e6ldyA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth H]	V-set_8	e6ldyH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth H]	C1-set_1	e6ldyH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E [auth L]	Light Chain	IGKV1	Kappa	methylated peptide	SAbDab (2025-12-19)
A, D [auth H]	Heavy Chain	IGHV1	-	methylated peptide	SAbDab (2025-12-19)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F [auth M]	Methylated peptide	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding kinase binding enzyme binding protein kinase binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine/threonine kinase activity MAP kinase kinase kinase activity cation binding metal ion binding protein serine kinase activity	cellular response to stimulus response to stimulus response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular process cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus regulation of biological process regulation of cellular process signaling biological regulation cellular response to stimulus response to stimulus response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular process cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus regulation of biological process regulation of cellular process signaling biological regulation signal transduction intracellular signal transduction cell communication	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B, E [auth L]	Fab light chain	-	-	-
A, D [auth H]	Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F [auth M]	IPR017441	Protein kinase, ATP binding site	Binding Site
C, F [auth M]	IPR034879	Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain	Domain
C, F [auth M]	IPR000270	PB1 domain	Domain
C, F [auth M]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C, F [auth M]	IPR053793	PB1-like domain	Domain
C, F [auth M]	IPR000719	Protein kinase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F [auth M]	Pharos: Q9Y2U5	ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis acute myeloid leukemia Blastic phase chronic myeloid leukemia glioblastoma interstitial lung disease lung large cell carcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma Pick disease tuberculosis astrocytic tumor idiopathic pulmonary fibrosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis acute myeloid leukemia Blastic phase chronic myeloid leukemia glioblastoma interstitial lung disease lung large cell carcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma Pick disease tuberculosis astrocytic tumor idiopathic pulmonary fibrosis juvenile dermatomyositis malignant ependymoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor atypical teratoid rhabdoid tumor diabetes mellitus large cell medulloblastoma malignant glioma myopathy

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, F [auth M]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.