4KRL | pdb_00004krl

Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 6.0

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A [auth B]	d4krlb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
B [auth A]	d4krla1	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	L domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d4krla2	Small proteins	Knottins (small inhibitors, toxins, lectins)	Growth factor receptor domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d4krla3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	L domain-like	8038760	3001010	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Growth factor receptor domain-like	8038763	3000398	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	PNP_UDP_1	e4krlB1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: PNP_UDP_1	ECOD (v294.1)
B [auth A]		e4krlA1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth A]	3.80.20.20	Alpha Beta	Alpha-Beta Horseshoe	24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'	Chain A	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 B]	Nanobody/VHH domain 7D12	VH	Lama glama (llama)	IGHV3S101, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202611-0)
B [auth A]	Epidermal Growth Factor Receptor (EGFR)	EGFR1	Homo sapiens (human)	EGFR*01	R-LIKE-DOMAIN EGFR (Pr28-459)	RPI	EGFR1	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth B]	Heavy Chain	IGHV1	-	epidermal growth factor receptor	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF01030	Receptor L domain (Recep_L_domain)	Receptor L domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Nanobody/VHH domain 7D12	-	-	-
B [auth A]	Epidermal growth factor receptor	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding protein phosphatase binding phosphatase binding enzyme binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding protein phosphatase binding phosphatase binding enzyme binding protein tyrosine kinase activity 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 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 cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding growth factor binding epidermal growth factor binding hormone binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein tyrosine kinase activator activity enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity protein serine/threonine kinase activity MAP kinase kinase kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity ATPase binding identical protein binding virus receptor activity exogenous protein binding epidermal growth factor receptor activity chromatin binding kinase binding DNA binding double-stranded DNA binding nucleic acid binding	developmental process multicellular organismal process gland development animal organ development salivary gland development anatomical structure morphogenesis multicellular organism development gland morphogenesis salivary gland morphogenesis anatomical structure development animal organ morphogenesis exocrine system development system development positive regulation of protein localization to plasma membrane developmental process multicellular organismal process gland development animal organ development salivary gland development anatomical structure morphogenesis multicellular organism development gland morphogenesis salivary gland morphogenesis anatomical structure development animal organ morphogenesis exocrine system development system development positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization intracellular protein localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery regulation of biological process protein localization to cell periphery protein localization to plasma membrane biological regulation positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of protein localization to plasma membrane xenobiotic transport transport establishment of localization positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification metabolic process regulation of phosphorus metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process cerebral cortex cell migration head development forebrain development brain development nervous system development pallium development cerebral cortex development telencephalon cell migration central nervous system development forebrain cell migration cell migration telencephalon development cell motility cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication regulation of cellular response to stress positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress regulation of nucleobase-containing compound metabolic process DNA repair DNA metabolic process nucleic acid metabolic process regulation of DNA repair positive regulation of DNA metabolic process DNA damage response regulation of DNA metabolic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process miRNA transcription positive regulation of biosynthetic process regulation of miRNA metabolic process miRNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process cell morphogenesis ossification digestive system development tube development digestive tract development tube morphogenesis digestive tract morphogenesis ERBB2 signaling pathway ERBB2-EGFR signaling pathway regulation of growth regulation of cellular component organization growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis positive regulation of cell communication positive regulation of signal transduction intracellular signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death protein kinase C signaling regulation of protein kinase C signaling positive regulation of protein kinase C signaling epithelium development epidermis development molting cycle process hair cycle tissue development skin development skin epidermis development hair follicle development molting cycle hair cycle process morphogenesis of an epithelial fold tissue morphogenesis morphogenesis of an epithelium cellular developmental process generation of neurons neurogenesis neuron differentiation cell differentiation placenta development chordate embryonic development embryo development in utero embryonic development embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation epithelial cell proliferation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid response to estradiol cellular response to estradiol stimulus membrane organization establishment of protein localization establishment of protein localization to membrane protein insertion into membrane regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway eyelid development in camera-type eye sensory organ development eye development visual system development camera-type eye development sensory system development cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to epidermal growth factor stimulus response to epidermal growth factor response to growth factor peptidyl-tyrosine modification regulation of peptidyl-tyrosine phosphorylation peptidyl-tyrosine phosphorylation positive regulation of DNA replication DNA replication regulation of DNA replication protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of ERBB signaling pathway positive regulation of epidermal growth factor receptor signaling pathway regulation of cell cycle phase transition cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle cell cycle regulation of cell cycle cell cycle process positive regulation of G1/S transition of mitotic cell cycle regulation of cell cycle process positive regulation of cell cycle regulation of mitotic cell cycle phase transition positive regulation of cell cycle G1/S phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle positive regulation of cell cycle phase transition G1/S transition of mitotic cell cycle mitotic cell cycle phase transition response to light stimulus response to radiation response to abiotic stimulus response to UV response to UV-A cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid negative regulation of protein catabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of metabolic process regulation of catabolic process regulation of protein catabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II regulation of developmental process regulation of cell differentiation negative regulation of cell differentiation regulation of multicellular organismal process negative regulation of cardiocyte differentiation heart development negative regulation of developmental process cardiocyte differentiation circulatory system development regulation of cardiocyte differentiation negative regulation of multicellular organismal process phosphatidylinositol 3-kinase/protein kinase B signal transduction fibroblast proliferation regulation of fibroblast proliferation positive regulation of fibroblast proliferation positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction import into cell ubiquitin-dependent endocytosis vesicle-mediated transport establishment of protein localization to organelle protein transport protein localization to organelle endocytosis behavior system process learning or memory nervous system process cognition cell adhesion cell-cell adhesion	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane intracellular vesicle membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane intracellular vesicle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane cytoplasm cytosol cell projection sperm principal piece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection protein-containing complex receptor complex Golgi membrane Golgi apparatus endosome membrane endosome extracellular region extracellular space intracellular membraneless organelle ciliary basal body microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton anchoring junction cell junction focal adhesion cell-substrate junction sperm end piece ruffle cell leading edge plasma membrane leading edge membrane cell periphery ruffle membrane plasma membrane region cell projection membrane basal part of cell basal plasma membrane cell surface membrane microdomain membrane raft organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane basolateral plasma membrane sperm midpiece perinuclear region of cytoplasm Shc-EGFR complex plasma membrane protein complex membrane protein complex multivesicular body, internal vesicle vesicle lumen multivesicular body, internal vesicle lumen endosomal intralumenal vesicle lumen membrane-enclosed lumen endosomal intralumenal vesicle intracellular organelle lumen organelle lumen late endosome multivesicular body early endosome early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR016245	Tyrosine protein kinase, EGF/ERB/XmrK receptor	Family
B [auth A]	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
B [auth A]	IPR000719	Protein kinase domain	Domain
B [auth A]	IPR032778	Growth factor receptor domain 4	Domain
B [auth A]	IPR006212	Furin-like repeat	Repeat
B [auth A]	IPR017441	Protein kinase, ATP binding site	Binding Site
B [auth A]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
B [auth A]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B [auth A]	IPR008266	Tyrosine-protein kinase, active site	Active Site
B [auth A]	IPR036941	Receptor L-domain superfamily	Homologous Superfamily
B [auth A]	IPR049328	Epidermal growth factor receptor-like, transmembrane-juxtamembrane segment	Domain
B [auth A]	IPR000494	Receptor L-domain	Domain
B [auth A]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth A]	IPR006211	Furin-like cysteine-rich domain	Domain
B [auth A]	IPR050122	Receptor Tyrosine Kinase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A]	Pharos: P00533	non-small cell lung carcinoma glioblastoma inflammatory skin and bowel disease, neonatal, 2 giant cell glioblastoma osteosarcoma lung cancer cholangiocarcinoma squamous cell carcinoma autosomal recessive polycystic kidney disease dilated cardiomyopathy breast cancer cancer esophageal squamous cell carcinoma classic familial adenomatous polyposis gliosarcoma non-small cell lung carcinoma glioblastoma inflammatory skin and bowel disease, neonatal, 2 giant cell glioblastoma osteosarcoma lung cancer cholangiocarcinoma squamous cell carcinoma autosomal recessive polycystic kidney disease dilated cardiomyopathy breast cancer cancer esophageal squamous cell carcinoma classic familial adenomatous polyposis gliosarcoma breast carcinoma malignant colon neoplasm ovarian cancer papilloma urinary bladder cancer adrenal cortex carcinoma squamous papilloma head and neck cancer tubular adenocarcinoma dermatitis head and neck squamous cell carcinoma Mammary Neoplasms, Experimental prostate cancer adenocarcinoma rectal cancer cervical cancer small cell lung carcinoma colorectal cancer malignant mesothelioma bile duct cancer type 2 diabetes mellitus intrahepatic cholangiocarcinoma gallbladder cancer granular cell carcinoma bile duct carcinoma endometriosis carcinoma esophageal cancer rectal neoplasm nasopharyngeal carcinoma sarcomatoid carcinoma malignant glioma cribriform carcinoma ovarian disease pancreatic ductal adenocarcinoma benign neoplasm of esophagus bile duct neoplasm malignant pancreatic neoplasm papillomatosis hepatocellular carcinoma brain disease urinary bladder disease pituitary cancer uterine disease endometrial carcinoma acute kidney failure interstitial cystitis maturity-onset diabetes of the young endometrium adenocarcinoma kidney disease laryngeal squamous cell carcinoma carcinoma of esophagus rheumatoid arthritis lung benign neoplasm nasopharyngeal neoplasm lung disease neoplasm of esophagus gastric cancer major depressive disorder squamous cell lung carcinoma Cowden syndrome 1 atypical teratoid rhabdoid tumor subependymal giant cell astrocytoma cribriform carcinoma of breast ovarian neoplasm head and neck carcinoma benign colon neoplasm pancreatic neoplasm bone disease malignant tumor of nasopharynx dilated cardiomyopathy 1A Pick disease brain glioma urinary bladder neoplasm ductal breast carcinoma in situ prostate disease medulloblastoma endometrium carcinoma in situ rectal carcinoma myopathy esophagus carcinoma in situ adrenal carcinoma sarcoidosis alcohol abuse small cell carcinoma colonic neoplasm neoplasm of neck gastric neoplasm spina bifida colorectal carcinoma autosomal dominant polycystic kidney disease tongue squamous cell carcinoma cutaneous lupus erythematosus pancreatic adenocarcinoma head and neck neoplasm benign mesothelioma undifferentiated carcinoma digestive system disease hematologic disease bone osteosarcoma malignant tumor of neck pilocytic astrocytoma hereditary diffuse gastric adenocarcinoma mammary neoplasms, animal prostate adenocarcinoma breast disease invasive ductal breast carcinoma large cell medulloblastoma mesothelioma lung adenocarcinoma exanthem lung carcinoma gallbladder neoplasm lymphatic system disease colorectal adenocarcinoma genetic intestinal polyposis oligodendroglioma glioma astrocytic tumor

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.