5NGV

CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, ORTHORHOMBIC CRYSTAL FORM

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)
A	d5ngva_	Small proteins	Snake toxin-like	Snake toxin-like	Extracellular domain of cell surface receptors	Type II activin receptor	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d5ngvh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d5ngvh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d5ngvl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d5ngvl2	Artifacts	Tags	Tags	Tags	C-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)
A	SCOP2B Superfamily	Snake toxin-like	8042166	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)
A	PF01064	e5ngvA1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: PF01064	ECOD (1.6)
B [auth H]	PF07686	e5ngvH1	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 L]	PF07686	e5ngvL1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

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	ActRIIB receptor	ACVR2B	Homo sapiens (human)	ACVR2B*01	R-LIKE-DOMAIN ACVR2B (Pr20-134)	IG	ACVR2B	IMGT (202416-0)
B [auth H]	Anti-human ActRIIB mAb BYM338	VH	Homo sapiens (human)	IGHV1-202, IGHJ401, IGHJ501, IGHJ502, IGHJ402, IGHJ403	V-DOMAIN VH	IG	VH_V-LAMBDA	IMGT (202416-0)
C [auth L]	Anti-human ActRIIB mAb BYM338	V-LAMBDA	Homo sapiens (human)	IGLV2-2301, IGLJ201, IGLJ302, IGLJ301	V-DOMAIN V-LAMBDA	IG	VH_V-LAMBDA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV1	-	activin receptor type-2b	SAbDab (2024-04-26)
C [auth L]	Light Chain	IGLV2	Lambda	activin receptor type-2b	SAbDab (2024-04-26)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B [auth H]	Bimagrumab	ACVR2B	Therapeutic SAbDab (2024-04-26)
C [auth L]	Bimagrumab	ACVR2B	Therapeutic SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	Activin receptor type-2B	protein-containing complex binding activin binding binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase regulator activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding protein-containing complex binding activin binding binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase regulator activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor 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 activin receptor activity, type II protein serine/threonine/tyrosine kinase activity protein binding growth factor binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development epithelium development endothelial cell differentiation cellular developmental process endothelium development lymphatic endothelial cell differentiation tissue development developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development epithelium development endothelial cell differentiation cellular developmental process endothelium development lymphatic endothelial cell differentiation tissue development epithelial cell differentiation vasculature development cell differentiation cellular process lymph vessel development digestive system development foregut morphogenesis tube development embryonic morphogenesis embryo development digestive tract development anatomical structure morphogenesis tube morphogenesis embryonic foregut morphogenesis digestive tract morphogenesis mesoderm development artery development blood vessel development regulation of developmental process positive regulation of biological 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 regulation of biological process bone mineralization biological regulation positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic 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 organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process skeletal system development skeletal system morphogenesis animal organ morphogenesis phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process kidney development renal system development protein localization establishment of protein localization cellular localization nitrogen compound transport transport signaling hormone secretion cell communication protein localization to extracellular region peptide secretion localization secretion by cell amide transport signal release cellular macromolecule localization regulation of biological quality secretion regulation of hormone levels organic substance transport establishment of protein localization to extracellular region cell-cell signaling export from cell protein secretion establishment of localization peptide transport protein transport peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of activin receptor signaling pathway cellular response to stimulus positive regulation of cell communication activin receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway positive regulation of signal transduction response to stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction positive regulation of response to stimulus signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of response to stimulus regulation of cell communication transforming growth factor beta receptor superfamily signaling pathway regulation of activin receptor signaling pathway positive regulation of signaling sensory organ development retina vasculature development in camera-type eye eye development retina development in camera-type eye visual system development camera-type eye development sensory system development 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 gastrulation with mouth forming second gastrulation developmental growth growth organ growth odontogenesis of dentin-containing tooth odontogenesis lymphangiogenesis anatomical structure formation involved in morphogenesis lymph vessel morphogenesis respiratory tube development lung development respiratory system development response to hexose response to organic substance response to monosaccharide response to carbohydrate response to glucose response to chemical response to oxygen-containing compound determination of bilateral symmetry pattern specification process determination of left/right symmetry left/right pattern formation regionalization specification of symmetry pancreas development blood vessel remodeling tissue remodeling regulation of osteoblast differentiation regulation of cell differentiation osteoblast differentiation positive regulation of osteoblast differentiation positive regulation of cell differentiation venous blood vessel development negative regulation of cold-induced thermogenesis homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis negative regulation of multicellular organismal process post-embryonic development anterior/posterior pattern specification roof of mouth development	intracellular anatomical structure cytoplasm cellular anatomical entity 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 intracellular anatomical structure cytoplasm cellular anatomical entity 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
B [auth H]	anti-human ActRIIB mAb BYM338 heavy-chain	-	-	-
C [auth L]	anti-human ActRIIB mAb BYM338 light-chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q13705	visceral heterotaxy situs inversus heterotaxy, visceral, 4, autosomal right atrial isomerism subependymal giant cell astrocytoma Asplenia Syndrome interstitial cystitis lung cancer osteosarcoma primitive neuroectodermal tumor situs ambiguus atrial fibrillation large cell medulloblastoma malignant mesothelioma Pick disease visceral heterotaxy situs inversus heterotaxy, visceral, 4, autosomal right atrial isomerism subependymal giant cell astrocytoma Asplenia Syndrome interstitial cystitis lung cancer osteosarcoma primitive neuroectodermal tumor situs ambiguus atrial fibrillation large cell medulloblastoma malignant mesothelioma Pick disease atypical teratoid rhabdoid tumor medulloblastoma

Protein Modification Annotation

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.