6FJ3 | pdb_00006fj3

High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Class B (secretin) G protein-coupled receptor-like	8091123	4007725	SCOP2 (2022-06-29)
A	SCOP2 Family	Hormone receptor domain	8091131	4003045	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	G protein-coupled receptor-like	8091124	3000473	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FnI-like domain	8091132	3000979	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Type B glycosyltransferase-like	8038006	3001586	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	7tm_2	e6fj3A3	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_2	ECOD (1.6)
A	Glycos_transf_1	e6fj3A1	A: a/b three-layered sandwiches	X: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	H: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: Glycos_transf_1	ECOD (1.6)
A	HRM	e6fj3A2	A: few secondary structure elements	X: Hormone receptor domain (HRM, Pfam 02793) (From Topology)	H: Hormone receptor domain (HRM, Pfam 02793) (From Topology)	T: Hormone receptor domain (HRM, Pfam 02793)	F: HRM	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01279	Parathyroid hormone family (Parathyroid)	Parathyroid hormone family	-	Family
A	PF13692	Glycosyl transferases group 1 (Glyco_trans_1_4)	Glycosyl transferases group 1		Domain
A	PF02793	Hormone receptor domain (HRM)	Hormone receptor domain	-	Family
A	PF00002	7 transmembrane receptor (Secretin family) (7tm_2)	7 transmembrane receptor (Secretin family)	This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs). They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognise ...	This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs). They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 (Swiss:P48960); calcium-independent receptors for latrotoxin (such as Swiss:O94910), and brain-specific angiogenesis inhibitors (such as Swiss:O14514) amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins (e.g. Swiss:P83119). Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Parathyroid hormone	parathyroid hormone receptor binding protein binding binding signaling receptor binding G protein-coupled receptor binding type 1 parathyroid hormone receptor binding peptide hormone receptor binding hormone receptor binding hormone activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	magnesium ion homeostasis inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis monoatomic cation homeostasis developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development magnesium ion homeostasis inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis monoatomic cation homeostasis developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development multicellular organismal-level homeostasis homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of biological process regulation of cellular process negative regulation of apoptotic process in bone marrow cell negative regulation of programmed cell death apoptotic process in bone marrow cell regulation of apoptotic process in bone marrow cell regulation of apoptotic process biological regulation 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 generation of precursor metabolites and energy positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of glycogen metabolic process positive regulation of metabolic process regulation of small molecule metabolic process small molecule metabolic process positive regulation of macromolecule metabolic process carbohydrate biosynthetic process hexose metabolic process positive regulation of glucose metabolic process positive regulation of glycogen biosynthetic process energy reserve metabolic process regulation of macromolecule biosynthetic process positive regulation of carbohydrate metabolic process regulation of glycogen metabolic process regulation of metabolic process monosaccharide metabolic process regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds regulation of glucan biosynthetic process positive regulation of biological process regulation of polysaccharide metabolic process polysaccharide metabolic process glucan metabolic process positive regulation of biosynthetic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process glycogen metabolic process generation of precursor metabolites and energy regulation of macromolecule metabolic process glycogen biosynthetic process regulation of polysaccharide biosynthetic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process phosphate ion homeostasis signaling cell-cell signaling cell communication intracellular calcium ion homeostasis calcium ion homeostasis cellular homeostasis intracellular monoatomic cation homeostasis intracellular chemical homeostasis intracellular monoatomic ion homeostasis regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process multicellular organism development positive regulation of biomineral tissue development regulation of multicellular organismal process regulation of multicellular organismal development positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification cellular response to stimulus response to stimulus adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction cell population proliferation positive regulation of cell population proliferation positive regulation of cell proliferation in bone marrow cell proliferation in bone marrow regulation of cell proliferation in bone marrow regulation of cell population proliferation negative regulation of metabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process regulation of localization hexose transmembrane transport D-glucose import transport carbohydrate transport positive regulation of D-glucose transmembrane transport localization positive regulation of transmembrane transport regulation of D-glucose import positive regulation of D-glucose import regulation of transport establishment of localization transmembrane transport regulation of transmembrane transport positive regulation of transport D-glucose transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport positive regulation of cell communication regulation of signaling positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus regulation of response to stimulus regulation of cell communication positive regulation of signaling regulation of leukocyte proliferation osteoclast proliferation regulation of osteoclast proliferation positive regulation of osteoclast proliferation leukocyte proliferation positive regulation of leukocyte proliferation positive regulation of DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of inositol phosphate biosynthetic process alcohol metabolic process positive regulation of phosphate metabolic process inositol phosphate metabolic process phosphate-containing compound metabolic process polyol biosynthetic process phosphorus metabolic process polyol metabolic process positive regulation of phosphorus metabolic process regulation of alcohol biosynthetic process small molecule biosynthetic process positive regulation of inositol phosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process inositol phosphate biosynthetic process alcohol biosynthetic process regulation of phosphorus metabolic process positive regulation of alcohol biosynthetic process	cellular anatomical structure extracellular region extracellular space
A	Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity amide binding peptide hormone binding hormone binding peptide receptor activity molecular transducer activity G protein-coupled receptor activity G protein-coupled peptide receptor activity signaling receptor activity transmembrane signaling receptor activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity amide binding peptide hormone binding hormone binding peptide receptor activity molecular transducer activity G protein-coupled receptor activity G protein-coupled peptide receptor activity signaling receptor activity transmembrane signaling receptor activity parathyroid hormone receptor activity UDP-glycosyltransferase activity alpha-1,4-glucan glucosyltransferase (NDP-glucose donor) activity glycosyltransferase activity alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity UDP-glucosyltransferase activity	developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development multicellular organism development skeletal system development system development cell population proliferation cellular process cellular response to stimulus developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development multicellular organism development skeletal system development system development cell population proliferation cellular process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis osteoblast development cellular developmental process cell differentiation cell development osteoblast differentiation embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development anatomical structure maturation cell maturation developmental maturation adenylate cyclase-activating G protein-coupled receptor signaling pathway positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process cell surface receptor signaling pathway negative regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process phospholipase C-activating G protein-coupled receptor signaling pathway connective tissue development chondrocyte differentiation cartilage development regulation of inositol phosphate biosynthetic process alcohol metabolic process positive regulation of phosphate metabolic process inositol phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process phosphate-containing compound metabolic process polyol biosynthetic process small molecule metabolic process phosphorus metabolic process regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process polyol metabolic process positive regulation of phosphorus metabolic process regulation of alcohol biosynthetic process small molecule biosynthetic process carbohydrate biosynthetic process primary metabolic process positive regulation of inositol phosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process inositol phosphate biosynthetic process alcohol biosynthetic process metabolic process regulation of phosphorus metabolic process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic process positive regulation of alcohol biosynthetic process multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane cytoplasm cytosol basal part of cell basal plasma membrane basolateral plasma membrane protein-containing complex receptor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001415	Parathyroid hormone/parathyroid hormone-related protein	Family
B	IPR003625	Parathyroid hormone	Family
A	IPR017983	GPCR, family 2, secretin-like, conserved site	Conserved Site
A	IPR050332	G-protein coupled receptor 2	Family
A	IPR036445	GPCR family 2, extracellular hormone receptor domain superfamily	Homologous Superfamily
A	IPR002170	GPCR, family 2, parathyroid hormone receptor	Family
A	IPR000832	GPCR, family 2, secretin-like	Family
A	IPR017981	GPCR, family 2-like, 7TM	Domain
A	IPR001879	GPCR, family 2, extracellular hormone receptor domain	Domain
A	IPR011835	Bacterial/plant glycogen synthase	Family
A	IPR013534	Starch synthase, catalytic domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q03431	Eiken syndrome metaphyseal chondrodysplasia, Jansen type rickets chondrodysplasia Blomstrand type Ollier disease primary failure of tooth eruption hyperparathyroidism medulloblastoma osteogenesis imperfecta psoriasis adrenal cortex adenoma breast carcinoma Glucocorticoid Induced Osteoporosis large cell medulloblastoma malignant glioma Eiken syndrome metaphyseal chondrodysplasia, Jansen type rickets chondrodysplasia Blomstrand type Ollier disease primary failure of tooth eruption hyperparathyroidism medulloblastoma osteogenesis imperfecta psoriasis adrenal cortex adenoma breast carcinoma Glucocorticoid Induced Osteoporosis large cell medulloblastoma malignant glioma postmenopausal osteoporosis adrenal cortex carcinoma hepatocellular carcinoma hypoparathyroidism lung disease malignant mesothelioma tooth ankylosis glioblastoma intellectual disability

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	GPCR Secretin (B) family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class B1	parathyroid hormone receptor-1 (PTH1R) in complex with a peptide agonist

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	AC5
B	AIB	Parent Component: ALA
B	HRG	Parent Component: ARG
B	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109
B	NLE	Parent Component: LEU RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100
A	YCM	Parent Component: CYS RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100

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.