2OR9 | pdb_00002or9

The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth H]	d2or9h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth I]	d2or9i1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]		e2or9L1	A: Profilin-like	X: sensor domains	H: sensor domains	T: HRM	F:	ECOD (20:10:01)
C [auth M]		e2or9M1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: DUF3239	F:	ECOD (20:10:01)
B [auth H]		e2or9H1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Copper-bind	F:	ECOD (20:10:01)
B [auth H]		e2or9H2	A: Profilin-like	X: sensor domains	H: sensor domains	T: HRM	F:	ECOD (20:10:01)
D [auth I]		e2or9I1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Copper-bind	F:	ECOD (20:10:01)
D [auth I]		e2or9I2	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: DUF3239	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth I]	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
A [auth L], C [auth M]	9E10	L-KAPPA	Mus musculus (house mouse)	IGKV3-201, IGKJ101, IGKJ102, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
B [auth H], D [auth I]	9E10	VH-CH1	Mus musculus (house mouse)	IGHV5-602, IGHJ401, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], C [auth M]	Light Chain	IGKV3	Kappa	synthetic epitope peptide of 9e10	SAbDab (2026-03-13)
B [auth H], D [auth I]	Heavy Chain	IGHV5	-	synthetic epitope peptide of 9e10	SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth L], C [auth M]	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
E [auth P]	PF02344	Myc leucine zipper domain (Myc-LZ)	Myc leucine zipper domain	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L], C [auth M]	Monoclonal anti-c-myc antibody 9E10	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
B [auth H], D [auth I]	Monoclonal anti-c-myc antibody 9E10	-	-	-
E [auth P]	synthetic epitope peptide of 9E10	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding protein dimerization activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity molecular function activator activity molecular function regulator activity transcription regulator activator activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding SCF ubiquitin ligase complex binding DNA-binding transcription factor binding E-box binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of transcription initiation by RNA polymerase II regulation of cellular process negative regulation of biological process 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 regulation of DNA-templated transcription initiation transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of transcription initiation by RNA polymerase II macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of DNA-templated transcription initiation response to chemical response to xenobiotic stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of stress-activated MAPK cascade regulation of cellular response to stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication stress-activated MAPK cascade regulation of intracellular signal transduction regulation of response to stress intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of stress-activated protein kinase signaling cascade regulation of MAPK cascade negative regulation of signal transduction regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus negative regulation of stress-activated protein kinase signaling cascade MAPK cascade regulation of cell communication negative regulation of MAPK cascade protein-DNA complex organization cellular component organization cellular component disassembly protein-containing complex organization protein-DNA complex disassembly protein-containing complex disassembly cellular component organization or biogenesis positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus response to hypoxia response to oxygen levels response to abiotic stimulus multicellular organismal process cell population proliferation cell activation lymphocyte activation NK T cell proliferation leukocyte proliferation NK T cell activation leukocyte activation T cell activation immune system process alpha-beta T cell proliferation mononuclear cell proliferation lymphocyte proliferation alpha-beta T cell activation T cell proliferation skeletal muscle cell differentiation developmental process cellular developmental process skeletal muscle tissue development animal organ development tissue development striated muscle tissue development muscle structure development skeletal muscle organ development cell differentiation anatomical structure development muscle tissue development muscle organ development striated muscle cell differentiation muscle cell differentiation myotube differentiation positive regulation of DNA-templated transcription positive regulation of miRNA transcription positive regulation of miRNA metabolic process miRNA transcription regulation of miRNA metabolic process miRNA metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of miRNA transcription fibroblast apoptotic process apoptotic process cell death programmed cell death mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process multicellular organism development anatomical structure morphogenesis skeletal system development skeletal system morphogenesis animal organ morphogenesis system development negative regulation of cell population proliferation fibroblast proliferation regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of fibroblast proliferation cellular response to xenobiotic stimulus pigmentation positive regulation of organelle organization regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization telomere organization positive regulation of telomere maintenance chromosome organization regulation of chromosome organization DNA metabolic process regulation of organelle organization positive regulation of chromosome organization telomere maintenance organelle organization positive regulation of DNA metabolic process regulation of DNA metabolic process myeloid leukocyte differentiation regulation of leukocyte differentiation regulation of developmental process cell development mononuclear cell differentiation regulation of cell differentiation regulation of cell development regulation of immune system process regulation of multicellular organismal process negative regulation of cell differentiation monocyte differentiation negative regulation of hemopoiesis negative regulation of monocyte differentiation regulation of multicellular organismal development regulation of monocyte differentiation negative regulation of leukocyte differentiation hemopoiesis regulation of myeloid cell differentiation negative regulation of developmental process regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development myeloid cell differentiation negative regulation of immune system process regulation of hemopoiesis negative regulation of multicellular organismal process leukocyte differentiation mesonephric epithelium development kidney epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development renal system development ureteric bud morphogenesis tube morphogenesis branching involved in ureteric bud morphogenesis renal tubule development epithelial tube morphogenesis nephron development nephron epithelium development ureteric bud development epithelium development tube development mesonephros development morphogenesis of an epithelium tissue morphogenesis kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis kidney development mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium negative regulation of cell division cell division regulation of cell division positive regulation of transcription by RNA polymerase II regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process positive regulation of programmed cell death regulation of B cell apoptotic process positive regulation of lymphocyte apoptotic process leukocyte apoptotic process regulation of apoptotic process B cell apoptotic process regulation of programmed cell death positive regulation of apoptotic process lymphocyte apoptotic process positive regulation of B cell apoptotic process positive regulation of leukocyte apoptotic process regulation of somatic stem cell population maintenance regulation of stem cell population maintenance stem cell population maintenance somatic stem cell population maintenance maintenance of cell number ear morphogenesis embryonic organ morphogenesis middle ear morphogenesis ear development sensory organ development embryonic morphogenesis embryo development sensory organ morphogenesis embryonic organ development negative regulation of gene expression via chromosomal CpG island methylation chromatin organization chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic acinar cell proliferation epithelial cell proliferation negative regulation of programmed cell death negative regulation of apoptotic process ERK1 and ERK2 cascade regulation of cell cycle process regulation of cell cycle positive regulation of cell population proliferation positive regulation of fibroblast proliferation positive regulation of cell communication positive regulation of signal transduction positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of intrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator intrinsic apoptotic signaling pathway positive regulation of intracellular signal transduction signal transduction by p53 class mediator apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling positive regulation of mesenchymal cell proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation protein maturation proteolysis protein processing protein metabolic process response to peptide response to interferon-alpha response to cytokine cellular response to cytokine stimulus cellular response to interferon-alpha regulation of kidney development metanephric cap morphogenesis mesenchyme development regulation of metanephric cap mesenchymal cell proliferation kidney mesenchyme development positive regulation of developmental process metanephros development metanephric mesenchyme morphogenesis positive regulation of cell proliferation involved in kidney development mesenchyme morphogenesis metanephric mesenchyme development positive regulation of kidney development cell proliferation involved in kidney development cell proliferation involved in metanephros development metanephric cap development positive regulation of metanephric cap mesenchymal cell proliferation positive regulation of multicellular organismal process metanephric cap mesenchymal cell proliferation involved in metanephros development kidney mesenchyme morphogenesis positive regulation of transcription initiation by RNA polymerase II positive regulation of DNA-templated transcription initiation detection of external stimulus system process nervous system process detection of mechanical stimulus involved in sensory perception of sound response to mechanical stimulus response to external stimulus detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus detection of stimulus involved in sensory perception sensory perception of sound intrinsic apoptotic signaling pathway in response to DNA damage response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation cellular response to abiotic stimulus cellular response to UV response to endogenous stimulus response to growth factor response to nitrogen compound response to alkaloid cell surface receptor signaling pathway Wnt signaling pathway regulation of acinar cell proliferation positive regulation of acinar cell proliferation rRNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle RNA polymerase II transcription repressor complex protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle RNA polymerase II transcription repressor complex protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle transcription repressor complex perinuclear region of cytoplasm cytoplasm cytoskeleton spindle microtubule cytoskeleton axon cell projection neuron projection plasma membrane bounded cell projection membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm RNA polymerase II transcription regulator complex Myc-Max complex euchromatin nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth L], C [auth M]	IPR050150	Immunoglobulin Variable Light Chain	Family
A [auth L], C [auth M]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth L], C [auth M]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth L], C [auth M]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth L], C [auth M]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth L], C [auth M]	IPR007110	Immunoglobulin-like domain	Domain
E [auth P]	IPR050433	Myc family transcription factors	Family
E [auth P]	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
E [auth P]	IPR002418	Transcription regulator Myc	Family
E [auth P]	IPR003327	Leucine zipper, Myc	Domain
E [auth P]	IPR012682	Transcription regulator Myc, N-terminal	Domain
E [auth P]	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth P]	Pharos: P01106	cancer Burkitt lymphoma acute myeloid leukemia medulloblastoma myelodysplastic syndrome osteosarcoma glioblastoma cleft palate neuroblastoma hypertrophic cardiomyopathy angiosarcoma ovarian cancer plasma cell myeloma granular cell carcinoma Chromosome Breakage cancer Burkitt lymphoma acute myeloid leukemia medulloblastoma myelodysplastic syndrome osteosarcoma glioblastoma cleft palate neuroblastoma hypertrophic cardiomyopathy angiosarcoma ovarian cancer plasma cell myeloma granular cell carcinoma Chromosome Breakage adult medulloblastoma cutaneous neuroendocrine carcinoma endometrial carcinoma malignant colon neoplasm giant cell glioblastoma carcinoma prostate cancer cervical cancer medullomyoblastoma with myogenic differentiation squamous cell carcinoma adenocarcinoma trabecular adenocarcinoma urinary bladder cancer autosomal dominant polycystic kidney disease gastric cancer primitive neuroectodermal tumor childhood medulloblastoma sarcomatoid carcinoma melanotic medulloblastoma tubular adenocarcinoma liver cancer non-small cell lung carcinoma B-cell chronic lymphocytic leukemia pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia exocrine pancreatic carcinoma lung disease bone disease breast cancer gastric neoplasm malignant glioma prostate adenocarcinoma hepatocellular carcinoma sinusitis hereditary diffuse gastric adenocarcinoma acute T cell leukemia colonic neoplasm stomach disease intestinal disease congestive heart failure undifferentiated carcinoma large cell medulloblastoma urinary bladder neoplasm oligodendroglioma ovarian carcinoma liver neoplasm atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous carcinoma lung benign neoplasm benign colon neoplasm pancreatic neoplasm bone osteosarcoma polycystic kidney disease 2 fatty liver disease breast disease hematologic disease psoriasis myopathy colorectal cancer invasive ductal breast carcinoma cribriform carcinoma desmoplastic/nodular medulloblastoma ovarian disease pancreatic intraductal papillary-mucinous neoplasm lung carcinoma benign neoplasm pilocytic astrocytoma eye disease lymphatic system disease brain disease malignant ependymoma prostate disease malignant pancreatic neoplasm cleft lip nasopharyngeal carcinoma common variable immunodeficiency kidney disease adrenal cortex carcinoma cribriform carcinoma of breast urinary bladder disease allergic rhinitis uterine disease liver disease astrocytic tumor ovarian neoplasm endometrial cancer lung adenocarcinoma

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.