Annotations: 4YHP

Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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 [auth A]	DUF5110	e4yhpA2	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)
B [auth A]	NTP_transferase	e4yhpA1	A: beta barrels	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NTP_transferase	ECOD (v294.2)
E [auth C]	DUF5110	e4yhpC2	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)
E [auth C]	NTP_transferase	e4yhpC3	A: beta barrels	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NTP_transferase	ECOD (v294.2)
G [auth E]	DUF5110	e4yhpE1	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)
G [auth E]	NTP_transferase	e4yhpE2	A: beta barrels	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NTP_transferase	ECOD (v294.2)
H	DUF5110	e4yhpH2	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)
H	NTP_transferase	e4yhpH1	A: beta barrels	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NTP_transferase	ECOD (v294.2)
C [auth B]	DUF5110	e4yhpB1	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)
F [auth D]	DUF5110	e4yhpD1	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)
I [auth L]	DUF5110	e4yhpL1	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)
J [auth F]	DUF5110	e4yhpF1	A: beta barrels	X: TIM beta/alpha-barrel	H: Glycoside hydrolase/deacetylase	T: Glycoside hydrolase/deacetylase	F: DUF5110	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth A], E [auth C], G [auth E], H	309M3-B Fab	VH-CH1	Homo sapiens (human)	IGHV3-701, IGHV3-702, IGHV3-703, IGHJ201, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_V-LAMBDA-C-KAPPA	IMGT (202617-0)
C [auth B], F [auth D], I [auth L], J [auth F]	309M3-B Fab	V-LAMBDA-C-KAPPA	Homo sapiens (human)	IGLV3-2102, IGLJ101, IGKC*01	V-DOMAIN V-LAMBDA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_V-LAMBDA-C-KAPPA	IMGT (202617-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth A], E [auth C], G [auth E], H	Heavy Chain	IGHV3	-	h3k9me3 peptide	SAbDab (2026-05-08)
C [auth B], F [auth D], I [auth L], J [auth F]	Light Chain	IGLV3	Lambda	h3k9me3 peptide	SAbDab (2026-05-08)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P], D [auth Q]	H3K9me3 peptide	DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth A], E [auth C], G [auth E], H	Fab Heavy Chain	-	-	-
C [auth B], F [auth D], I [auth L], J [auth F]	Fab Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth P], D [auth Q]	IPR009072	Histone-fold	Homologous Superfamily
A [auth P], D [auth Q]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A [auth P], D [auth Q]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth P], D [auth Q]	: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth P], D [auth Q]	M3L	Parent Component: LYS : AA0074 : N6,N6,N6-trimethyl-L-lysine MOD:00083

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.