5NH3 | pdb_00005nh3

CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV

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
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth M]	d5nh3m1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth M]	d5nh3m2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth L]	d5nh3l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth L]	d5nh3l2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth I]	d5nh3i1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth I]	d5nh3i2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d5nh3h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d5nh3h2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5nh3b_	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5nh3a_	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	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)
B	SCOP2 Family	Extracellular domain of cell surface receptors	8079336	4003329	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Snake toxin-like	8079337	3000545	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Snake toxin-like	8079337	3000545	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 M]	V-set_3	e5nh3M1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
E [auth L]	V-set_3	e5nh3L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D [auth I]	V-set_8	e5nh3I1	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 H]	V-set_8	e5nh3H1	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)
B	Activin_recp	e5nh3B1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: Activin_recp	ECOD (1.6)
A	Activin_recp	e5nh3A1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: Activin_recp	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
A	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	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
E [auth L], F [auth M]	mAb BYM338, anti-human ActRIIB	V-LAMBDA	Homo sapiens (human)	IGLV2-2302, IGLJ201, IGLJ302, IGLJ301	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202546-0)
C [auth H], D [auth I]	mAb BYM338, anti-human ActRIIB	VH	Homo sapiens (human)	IGHV1-206, IGHJ401, IGHJ402, IGHJ403	V-DOMAIN VH	IG	FV-HEAVY_LAMBDA	IMGT (202546-0)
A, B	Activin receptor type-2A	ACVR2A	Homo sapiens (human)	ACVR2A*01	R-LIKE-DOMAIN ACVR2A (Pr21-128)	FPIA	ACVR2A	IMGT (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth L], F [auth M]	Light Chain	IGLV2	Lambda	activin receptor type-2a	SAbDab (2025-11-28)
C [auth H], D [auth I]	Heavy Chain	IGHV1	-	activin receptor type-2a	SAbDab (2025-11-28)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
E [auth L], F [auth M]	Bimagrumab	ACVR2B	Therapeutic SAbDab (2025-11-28)
C [auth H], D [auth I]	Bimagrumab	ACVR2B	Therapeutic SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01064	Activin types I and II receptor domain (Activin_recp)	Activin types I and II receptor domain	This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The t ...	This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth L], F [auth M]	anti-human ActRIIB mAb BYM338 Fv light-chain	-	-	-
C [auth H], D [auth I]	anti-human ActRIIB mAb BYM338 Fv heavy-chain	-	-	-
A, B	Activin receptor type-2A	molecular transducer activity coreceptor activity signaling receptor activity protein-containing complex binding activin binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding molecular transducer activity coreceptor activity signaling receptor activity protein-containing complex binding activin binding binding 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 protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity activin receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane receptor protein serine/threonine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity cation binding metal ion binding identical protein binding protein binding activin receptor activity, type II PDZ domain binding protein domain specific binding inhibin binding growth factor binding BMP receptor activity activin receptor activity, type I	cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling developmental process multicellular organism development multicellular organismal process anatomical structure development pattern specification process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation tissue development mesoderm development Sertoli cell proliferation cell population proliferation gonad development reproductive system development sex differentiation animal organ development male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development epithelial cell proliferation system development regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process positive regulation of biomineral tissue development ossification biomineral tissue development regulation of multicellular organismal process regulation of multicellular organismal development bone mineralization positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification multi-multicellular organism process sperm ejaculation mating behavior behavior reproductive behavior insemination multi-organism reproductive process copulation cellular developmental process homeostatic process cell development regulation of cell differentiation regulation of cell development positive regulation of cell differentiation cell differentiation regulation of immune system process myeloid cell homeostasis erythrocyte homeostasis hemopoiesis regulation of myeloid cell differentiation erythrocyte differentiation regulation of erythrocyte differentiation positive regulation of erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostasis of number of cells embryo development ending in birth or egg hatching skeletal system development chordate embryonic development embryonic skeletal system development embryo development positive regulation of DNA-templated transcription RNA 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic 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 activin receptor signaling pathway activin receptor signaling pathway transforming growth factor beta receptor superfamily signaling pathway regulation of activin receptor signaling pathway osteoblast differentiation cellular response to BMP stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus response to BMP response to growth factor BMP signaling pathway anatomical structure morphogenesis gastrulation with mouth forming second embryonic morphogenesis gastrulation odontogenesis of dentin-containing tooth odontogenesis animal organ morphogenesis penile erection regulation of nitric oxide biosynthetic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process regulation of nitric oxide metabolic process determination of bilateral symmetry determination of left/right symmetry left/right pattern formation regionalization specification of symmetry regulation of osteoblast differentiation positive regulation of osteoblast differentiation positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of protein modification process phosphate-containing compound 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 macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation anterior/posterior pattern specification	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex receptor complex catalytic complex plasma membrane protein complex membrane plasma membrane membrane protein complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups cell periphery cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex receptor complex catalytic complex plasma membrane protein complex membrane plasma membrane membrane protein complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups cell periphery serine/threonine protein kinase complex plasma membrane signaling receptor complex activin receptor complex cell surface inhibin-betaglycan-ActRII complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000472	Activin types I and II receptor domain	Domain
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR000333	Ser/Thr protein kinase, TGFB receptor	Family
A, B	IPR045860	Snake toxin-like superfamily	Homologous Superfamily
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P27037	Microsatellite Instability acute myeloid leukemia breast cancer gastric adenocarcinoma invasive ductal breast carcinoma pilocytic astrocytoma astrocytic tumor breast carcinoma glioblastoma malignant ependymoma osteosarcoma atypical teratoid rhabdoid tumor endogenous depression interstitial cystitis malignant glioma Microsatellite Instability acute myeloid leukemia breast cancer gastric adenocarcinoma invasive ductal breast carcinoma pilocytic astrocytoma astrocytic tumor breast carcinoma glioblastoma malignant ependymoma osteosarcoma atypical teratoid rhabdoid tumor endogenous depression interstitial cystitis malignant glioma ovarian cancer ulcerative colitis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth H], D [auth I]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.