6UMX

Structural basis for specific inhibition of extracellular activation of pro/latent myostatin by SRK-015

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 L]	d6umxl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d6umxl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d6umxh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], 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)
A	SCOP2B Superfamily	pro-TGF beta-like	8089964	3002405	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	pro-TGF beta-like	8089964	3002405	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	PF00688	e6umxA2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF00688	ECOD (1.6)
A	PF00019	e6umxA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00019	ECOD (1.6)
F [auth B]	PF00688	e6umxB2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF00688	ECOD (1.6)
F [auth B]	PF00019	e6umxB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00019	ECOD (1.6)
D [auth l]	PF07654	e6umxl2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth l]	PF07686	e6umxl1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth L]	PF07654	e6umxL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth L]	PF07686	e6umxL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth H]	PF07654	e6umxH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth H]	PF07686	e6umxH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth h]	PF07654	e6umxh1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth h]	PF07686	e6umxh2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

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 L], D [auth l]	-	L-LAMBDA	-	IGLV1-4401, IGLJ201, IGLJ302, IGLJ101, IGLJ301, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202417-0)
C [auth H], E [auth h]	-	VH-CH1	-	IGHV3-3003, IGHV3-3006, IGHV3-3012, IGHV3-3019, IGHV3-3305, IGHJ601, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202417-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], D [auth l]	Light Chain	IGLV1	Lambda	growth/differentiation factor 8	SAbDab (2024-05-03)
C [auth H], E [auth h]	Heavy Chain	IGHV3	-	growth/differentiation factor 8	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F [auth B]	PF00688	TGF-beta propeptide (TGFb_propeptide)	TGF-beta propeptide	-	Family
A, F [auth B]	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain	-	Domain
B [auth L], D [auth l]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
C [auth H], E [auth h]	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
C [auth H], E [auth h]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, F [auth B]	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 organic substance response to hormone response to chemical response to endogenous stimulus response to estrogen skeletal muscle cell differentiation developmental process cellular developmental process skeletal muscle tissue development animal organ development 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 organic substance 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 response to organonitrogen compound 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 cellular response to organonitrogen compound 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 macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic 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 biosynthetic 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
B [auth L], D [auth l]	GL29H4-16 Fab Light Chain,GL29H4-16 Fab Light Chain	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process	extracellular region extracellular space cellular anatomical entity blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular region extracellular space cellular anatomical entity blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex protein-containing complex immunoglobulin complex
C [auth H], E [auth h]	GL29H4-16 Fab Heavy Chain,GL29H4-16 Fab Heavy Chain	-	-	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth B]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, F [auth B]	IPR015615	Transforming growth factor-beta-related	Family
A, F [auth B]	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
A, F [auth B]	IPR001111	TGF-beta, propeptide	Domain
A, F [auth B]	IPR001839	Transforming growth factor-beta, C-terminal	Domain
B [auth L], D [auth l]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L], D [auth l]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L], D [auth l]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L], D [auth l]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], D [auth l]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth H], E [auth h]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H], E [auth h]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H], E [auth h]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H], E [auth h]	IPR003599	Immunoglobulin subtype	Domain
C [auth H], E [auth h]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth H], E [auth h]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H], E [auth h]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, F [auth B]	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 R01GM133198.