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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   LIRAGLUTIDE

Authors :   S. Ludvigsen, D. B. Steensgaard, J. K. Thomsen, H. Strauss, M. Normann

Date :   02 Apr 12 (Deposition) - 10 Jul 13 (Release) - 29 Jan 14 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Hormone, Glucagon, Glucagon Like Peptide-1 Analog (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. B. Steensgaard, J. K. Thomsen, H. Strauss, M. Normann, S. Ludvigsen
Liraglutide
To Be Published
PubMed: search

Molecule 1 - LIRAGLUTIDE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Taxid	:	4932
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	LIRAGLUTIDE IS A HUMAN GLP-1 ANALOG
	Synonym	:	GLUCAGON-LIKE PEPTIDE 1(7-37)

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	D6M	1	Ligand/Ion	N-HEXADECANOYL-L-GLUTAMIC ACID

NMR Structure * (1, 1)

No.	Name	Count	Type	Full Name
1	D6M	1	Ligand/Ion	N-HEXADECANOYL-L-GLUTAMIC ACID

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:25 , LYS A:26 , PHE A:28 , ILE A:29 , TRP A:31 , LEU A:32 , VAL A:33	BINDING SITE FOR RESIDUE D6M A1038

(no "SS Bond" information available for 4APD)

(no "Cis Peptide Bond" information available for 4APD)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014596	A	115	V	GLUC_HUMAN	Polymorphism	5650	A	A	24	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure * (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014596	A	115	V	GLUC_HUMAN	Polymorphism	5650	A	A	24	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUCAGON	PS00260	Glucagon / GIP / secretin / VIP family signature.	GLUC_HUMAN	53-75 92-114 98-120 146-168	1	- - A:7-29 -

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUCAGON	PS00260	Glucagon / GIP / secretin / VIP family signature.	GLUC_HUMAN	53-75 92-114 98-120 146-168	1	- - A:7-29 -

(no "Exon" information available for 4APD)

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:31
 aligned with GLUC_HUMAN | P01275 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:31
                                   107       117       127 
           GLUC_HUMAN    98 HAEGTFTSDVSSYLEGQAAKEFIAWLVKGRG 128
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------V------------- SAPs(SNPs)
                PROSITE (1) GLUCAGON  PDB: - -------------- PROSITE (1)
                PROSITE (2) GLUCAGON  PDB: A:7-29  -------- PROSITE (2)
                 Transcript ------------------------------- Transcript
                 4apd A   7 HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRG  37
                                    16        26        36

Chain A from PDB  Type:PROTEIN  Length:31
 aligned with U3KRF3_YEASX | U3KRF3 from UniProtKB/TrEMBL  Length:31

    Alignment length:31
                                    10        20        30 
         U3KRF3_YEASX     1 HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRG  31
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------V------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 4apd A   7 HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRG  37
                                    16        26        36

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4APD)

(no "CATH Domain" information available for 4APD)

(no "Pfam Domain" information available for 4APD)

NMR Structure(hide GO term definitions)

Chain A (U3KRF3_YEASX | U3KRF3)

molecular function
	GO:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A (GLUC_HUMAN | P01275)

molecular function
	GO:0031769	glucagon receptor binding	Interacting selectively and non-covalently with a glucagon receptor.
	GO:0005179	hormone activity	The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0007188	adenylate cyclase-modulating G-protein coupled receptor signaling pathway	The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation or inhibition of adenylyl cyclase activity and a subsequent change in the concentration of cyclic AMP (cAMP).
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0071377	cellular response to glucagon stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
	GO:0007631	feeding behavior	Behavior associated with the intake of food.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0032099	negative regulation of appetite	Any process that reduces appetite.
	GO:1900118	negative regulation of execution phase of apoptosis	Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.
	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0030819	positive regulation of cAMP biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0090280	positive regulation of calcium ion import	Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
	GO:0035948	positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0051571	positive regulation of histone H3-K4 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:0035774	positive regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0010800	positive regulation of peptidyl-threonine phosphorylation	Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
	GO:0032092	positive regulation of protein binding	Any process that activates or increases the frequency, rate or extent of protein binding.
	GO:0045860	positive regulation of protein kinase activity	Any process that activates or increases the frequency, rate or extent of protein kinase activity.
	GO:0010737	protein kinase A signaling	A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
	GO:0050796	regulation of insulin secretion	Any process that modulates the frequency, rate or extent of the regulated release of insulin.
	GO:0042594	response to starvation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0034774	secretory granule lumen	The volume enclosed by the membrane of a secretory granule.

NMR Structure
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	GLUC_HUMAN \| P01275	:	1bh0 1d0r 1nau 2g49 2l63 2l64 2m5p 2m5q 3iol 4zgm 5vai

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Description

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Ligands, Modified Residues, Ions (1, 1)

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