4EDX | pdb_00004edx

Nerve Growth Factor in Complex with Fab from mouse mAb 911

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
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)
F [auth H]	d4edxh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth B]	d4edxb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth L]	d4edxl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth L]	d4edxl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth A]	d4edxa2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth A]	d4edxa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth V]	d4edxv_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Neurotrophin	beta-Nerve growth factor	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth W]	d4edxw_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Neurotrophin	beta-Nerve growth factor	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)
D [auth V]	SCOP2B Superfamily	Cystine-knot cytokines	8038796	3000846	SCOP2B (2022-06-29)
A [auth W]	SCOP2B Superfamily	Cystine-knot cytokines	8038796	3000846	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)
F [auth H]		e4edxH1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F:	ECOD (develop294)
C [auth B]		e4edxB1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F:	ECOD (develop294)
E [auth L]		e4edxL1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F:	ECOD (develop294)
B [auth A]		e4edxA1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F:	ECOD (develop294)
D [auth V]		e4edxV1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F:	ECOD (develop294)
A [auth W]		e4edxW1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth 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)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth V]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
A [auth W]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	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
C [auth B], F [auth H]	Fab anti-NGF	VH-CH1	Mus musculus (house mouse)	IGHV2-6-701, IGHV2-6-702, IGHJ201, IGHG2A01, IGHG2A*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202610-0)
B [auth A], E [auth L]	Fab anti-NGF	L-KAPPA	Mus musculus (house mouse)	IGKV10-9601, IGKV10-9602, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth B], F [auth H]	Heavy Chain	IGHV2	-	beta-nerve growth factor	SAbDab (2026-03-20)
B [auth A], E [auth L]	Light Chain	IGKV10	Kappa	beta-nerve growth factor	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B], F [auth H]	heavy chain of Fab of murine anti-NGF	-	-	-
B [auth A], E [auth L]	light chain of FAB of murine anti-NGF	-	-	-
A [auth W], D [auth V]	Beta-nerve growth factor	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding nerve growth factor receptor binding cytokine receptor binding neurotrophin receptor binding tumor necrosis factor receptor superfamily binding death receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding nerve growth factor receptor binding cytokine receptor binding neurotrophin receptor binding tumor necrosis factor receptor superfamily binding death receptor binding protein tyrosine kinase activator activity enzyme regulator activity transmembrane receptor protein tyrosine kinase activator activity protein kinase regulator activity kinase activator activity enzyme activator activity protein kinase activator activity kinase regulator activity molecular function inhibitor activity peptidase regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity metalloendopeptidase inhibitor activity endopeptidase inhibitor activity lipid binding	cellular response to stimulus regulation of biological process cellular response to growth factor stimulus regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus biological regulation cellular response to nerve growth factor stimulus cell communication cellular response to endogenous stimulus nerve growth factor signaling pathway neurotrophin signaling pathway cellular response to stimulus regulation of biological process cellular response to growth factor stimulus regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus biological regulation cellular response to nerve growth factor stimulus cell communication cellular response to endogenous stimulus nerve growth factor signaling pathway neurotrophin signaling pathway response to nerve growth factor cellular process response to growth factor signal transduction rhythmic process circadian rhythm positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process axon extension multicellular organismal process positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth system development developmental process regulation of cell projection organization positive regulation of cell development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis cellular component organization regulation of axon extension regulation of nervous system development neurogenesis regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axon extension cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of protein modification process protein ubiquitination protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process primary metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of localization cellular localization transport modulation of chemical synaptic transmission localization synaptic signaling regulation of secretion by cell secretion by cell signal release establishment of localization in cell trans-synaptic signaling neurotransmitter secretion regulation of transport secretion regulation of neurotransmitter transport export from cell cell-cell signaling neurotransmitter transport establishment of localization regulation of secretion chemical synaptic transmission signal release from synapse regulation of trans-synaptic signaling regulation of neurotransmitter secretion anterograde trans-synaptic signaling positive regulation of neuron projection development signal transduction in absence of ligand extrinsic apoptotic signaling pathway in absence of ligand positive regulation of neuron differentiation regulation of neuron differentiation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation peripheral nervous system development positive regulation of collateral sprouting regulation of collateral sprouting collateral sprouting cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway neurotrophin TRK receptor signaling pathway nerve development positive regulation of cell maturation regulation of neuron maturation cell maturation regulation of cell maturation positive regulation of neuron maturation developmental maturation anatomical structure maturation neuron maturation system process sensory perception nervous system process sensory perception of pain regulation of calcium ion transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction regulation of Ras protein signal transduction positive regulation of Ras protein signal transduction Ras protein signal transduction positive regulation of small GTPase mediated signal transduction	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle extracellular region axon extracellular space endosome intracellular vesicle cytoplasmic vesicle endosome lumen vesicle transport vesicle synapse presynapse synaptic vesicle cell junction secretory vesicle exocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth W], D [auth V]	IPR020408	Nerve growth factor-like	Family
A [auth W], D [auth V]	IPR019846	Nerve growth factor conserved site	Conserved Site
A [auth W], D [auth V]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A [auth W], D [auth V]	IPR020437	Nerve growth factor, beta subunit, mammalian	Family
A [auth W], D [auth V]	IPR002072	Nerve growth factor-related	Domain
A [auth W], D [auth V]	IPR020425	Nerve growth factor, beta subunit	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth W], D [auth V]	Pharos: P01138	hereditary sensory and autonomic neuropathy type 5 peripheral neuropathy neurodegenerative disease glomerulonephritis status epilepticus Nerve Degeneration corneal ulcer cystitis epilepsy with generalized tonic-clonic seizures interstitial nephritis peripheral nervous system disease Lewy body dementia middle cerebral artery infarction cocaine abuse nervous system disorder hereditary sensory and autonomic neuropathy type 5 peripheral neuropathy neurodegenerative disease glomerulonephritis status epilepticus Nerve Degeneration corneal ulcer cystitis epilepsy with generalized tonic-clonic seizures interstitial nephritis peripheral nervous system disease Lewy body dementia middle cerebral artery infarction cocaine abuse nervous system disorder overactive bladder dissociative amnesia Parkinson disease chronic kidney disease hereditary sensory and autonomic neuropathy hereditary sensory and autonomic neuropathy type 4 cocaine dependence heroin dependence visual epilepsy malignant mesothelioma hereditary sensory and autonomic neuropathy type 1 chronic renal failure syndrome sensory peripheral neuropathy depressive disorder toxic encephalopathy autosomal recessive juvenile Parkinson disease 2 phaeochromocytoma Riley-Day syndrome Charcot-Marie-Tooth disease heart disease hereditary sensory and autonomic neuropathy type 2 hydrolethalus syndrome alcohol withdrawal amnestic disorder cancer cystic fibrosis parkinsonian disorder intellectual disability cerebrovascular disorder

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.