5F3B

Structure of myostatin in complex with chimeric RK35 antibody

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	d5f3ba_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth E]	d5f3be_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5f3bb2	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	d5f3bb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth F]	d5f3bf2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth F]	d5f3bf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth C]	d5f3bc_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d5f3bd_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	automated matches	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)
E [auth C]	SCOP2B Superfamily	Cystine-knot cytokines	8070309	3000846	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Cystine-knot cytokines	8070309	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)
A	V-set_8	e5f3bA1	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	e5f3bA2	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)
C [auth E]	V-set_8	e5f3bE1	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)
C [auth E]	C1-set_1	e5f3bE2	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)
B	C1-set_4	e5f3bB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e5f3bB1	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)
D [auth F]	C1-set_4	e5f3bF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth F]	V-set	e5f3bF1	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 C]	TGF_beta	e5f3bC1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)
F [auth D]	TGF_beta	e5f3bD1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth C]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
F [auth D]	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
A, C [auth E]	RK35 Fab	VH-CH1	Chimeric (chimeric)	IGHV5-9-301, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)
B, D [auth F]	RK35 Fab	L-KAPPA	Chimeric (chimeric)	IGKV6-1701, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C [auth E]	Heavy Chain	IGHV5	-	growth/differentiation factor 8	SAbDab (2024-10-25)
B, D [auth F]	Light Chain	IGKV6	Kappa	growth/differentiation factor 8	SAbDab (2024-10-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C], F [auth D]	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth E]	RK35 Chimeric antibody heavy chain	-	-	-
B, D [auth F]	RK35 Chimeric antibody light chain	-	-	-
E [auth C], F [auth D]	Growth/differentiation factor 8	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding protein homodimerization activity protein dimerization activity cytokine activity heparin binding protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding protein homodimerization activity protein dimerization activity cytokine activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	response to stimulus response to activity response to muscle activity muscle hypertrophy multicellular organismal process regulation of biological process system process negative regulation of muscle hypertrophy regulation of system process negative regulation of biological process biological regulation regulation of muscle system process muscle system process regulation of muscle hypertrophy response to stimulus response to activity response to muscle activity muscle hypertrophy multicellular organismal process regulation of biological process system process negative regulation of muscle hypertrophy regulation of system process negative regulation of biological process biological regulation regulation of muscle system process muscle system process regulation of muscle hypertrophy regulation of multicellular organismal process negative regulation of multicellular organismal process response to hormone response to endogenous stimulus response to chemical response to estrogen 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 cellular process muscle tissue development muscle organ development skeletal muscle satellite cell differentiation regulation of cellular process regulation of developmental process regulation of cell differentiation regulation of skeletal muscle cell differentiation negative regulation of cellular process negative regulation of skeletal muscle cell differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of satellite cell differentiation response to ketone response to lipid response to oxygen-containing compound response to testosterone response to organic cyclic compound response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus negative regulation of myoblast differentiation regulation of myoblast differentiation myoblast differentiation muscle atrophy striated muscle adaptation skeletal muscle atrophy muscle adaptation skeletal muscle adaptation striated muscle atrophy negative regulation of cell population proliferation cell population proliferation negative regulation of skeletal muscle satellite cell proliferation negative regulation of skeletal muscle cell proliferation skeletal muscle satellite cell proliferation regulation of cell population proliferation muscle cell proliferation regulation of skeletal muscle satellite cell proliferation skeletal muscle cell proliferation regulation of skeletal muscle cell proliferation striated muscle cell proliferation regulation of growth developmental growth negative regulation of growth regulation of skeletal muscle tissue growth regulation of developmental growth growth negative regulation of developmental growth skeletal muscle tissue growth negative regulation of skeletal muscle tissue growth cellular response to endogenous stimulus response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to organic cyclic compound cellular response to glucocorticoid stimulus cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to lipid response to dexamethasone cellular response to nitrogen compound negative regulation of signaling signaling response to peptide hormone regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus negative regulation of cell communication cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus regulation of insulin receptor signaling pathway cellular response to peptide hormone stimulus response to nitrogen compound negative regulation of signal transduction negative regulation of cellular response to insulin stimulus regulation of response to stimulus negative regulation of insulin receptor signaling pathway response to insulin regulation of cell communication cellular response to insulin stimulus response to alcohol response to ethanol positive regulation of locomotion regulation of cell motility macrophage migration positive regulation of chemotaxis positive regulation of cell migration taxis cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process chemotaxis regulation of leukocyte chemotaxis positive regulation of macrophage migration regulation of leukocyte migration response to external stimulus positive regulation of leukocyte chemotaxis granulocyte migration leukocyte migration regulation of locomotion regulation of response to external stimulus macrophage chemotaxis positive regulation of biological process positive regulation of response to stimulus regulation of granulocyte chemotaxis regulation of macrophage migration positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration cell motility locomotion positive regulation of cellular process cell chemotaxis regulation of macrophage chemotaxis positive regulation of leukocyte migration regulation of chemotaxis immune system process granulocyte chemotaxis mononuclear cell migration positive regulation of macrophage chemotaxis leukocyte chemotaxis response to electrical stimulus regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of intracellular signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process myoblast proliferation regulation of myoblast proliferation negative regulation of myoblast proliferation rhythmic process ovulation cycle ovulation cycle process reproductive process multicellular organismal reproductive process response to gravity regulation of cellular component organization positive regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization cellular component assembly regulation of lamellipodium assembly regulation of lamellipodium organization positive regulation of cell projection organization cellular component organization or biogenesis lamellipodium assembly plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly positive regulation of lamellipodium assembly regulation of cellular component biogenesis positive regulation of lamellipodium organization regulation of plasma membrane bounded cell projection assembly lamellipodium organization cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway cellular homeostasis homeostatic process muscle cell cellular homeostasis tissue regeneration skeletal muscle tissue regeneration regeneration myoblast migration involved in skeletal muscle regeneration muscle cell migration myoblast migration	extracellular region extracellular space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C], F [auth D]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
E [auth C], F [auth D]	IPR015615	Transforming growth factor-beta-related	Family
E [auth C], F [auth D]	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
E [auth C], F [auth D]	IPR001111	TGF-beta, propeptide	Domain
E [auth C], F [auth D]	IPR001839	Transforming growth factor-beta, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth C], F [auth D]	Pharos: O14793	myostatin-related muscle hypertrophy congestive heart failure astrocytic tumor Heart Decompensation myopathy psoriasis beta thalassemia heart failure malignant ependymoma myelodysplastic syndrome malignant glioma oligodendroglioma

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.