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Theoretical Model (Jmol Viewer)

Title :   MODEL OF MELANOCORTIN-4 RECEPTOR WITH AGRP

Authors :   I. D. Pogozheva

Date :   14 Oct 06 (Deposition) - 24 Oct 06 (Release) - 24 Oct 06 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B

Keywords :   G Protein-Coupled Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. X. Chai, I. D. Pogozheva, Y-M. Lai, R. R. Neubig, H. I. Mosberg, I. Gantz
Receptor-Antagonist Interactions In The Complexes Of Agouti And Agouti-Related Protein With Human Melanocortin 1 And 4 Receptors
Biochemistry V. 44 3418 2005
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MELANOCORTIN-4 RECEPTOR
	Chains	:	A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS

Molecule 2 - AGOUTI-RELATED PROTEIN
	Chains	:	B
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2IQV)

(no "Site" information available for 2IQV)

Theoretical Model

No.	Residues
1	A:40	-	A:279
2	A:271	-	A:277
3	B:87	-	B:102
4	B:94	-	B:108
5	B:101	-	B:119
6	B:105	-	B:129
7	B:110	-	B:117

(no "Cis Peptide Bond" information available for 2IQV)

Theoretical Model (28, 28)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_038634	V	50	M	MC4R_HUMAN	Disease (OBESITY)	121913557	A	V	50	M
02	UniProt	VAR_038635	S	58	C	MC4R_HUMAN	Disease (OBESITY)	121913558	A	S	58	C
03	UniProt	VAR_038636	N	62	S	MC4R_HUMAN	Disease (OBESITY)	121913566	A	N	62	S
04	UniProt	VAR_077570	N	72	K	MC4R_HUMAN	Disease	---	A	N	72	K
05	UniProt	VAR_010706	P	78	L	MC4R_HUMAN	Disease (OBESITY)	13447326	A	P	78	L
06	UniProt	VAR_038638	N	97	D	MC4R_HUMAN	Disease (OBESITY)	121913565	A	N	97	D
07	UniProt	VAR_038639	I	102	S	MC4R_HUMAN	Disease (OBESITY)	121913559	A	I	102	S
08	UniProt	VAR_038640	I	102	T	MC4R_HUMAN	Disease (OBESITY)	121913559	A	I	102	T
09	UniProt	VAR_010707	V	103	I	MC4R_HUMAN	Polymorphism	2229616	A	I	103	I
10	UniProt	VAR_038641	L	106	P	MC4R_HUMAN	Disease (OBESITY)	---	A	L	106	P
11	UniProt	VAR_010708	T	112	M	MC4R_HUMAN	Polymorphism	13447329	A	T	112	M
12	UniProt	VAR_038642	I	125	K	MC4R_HUMAN	Disease (OBESITY)	---	A	I	125	K
13	UniProt	VAR_038643	S	127	L	MC4R_HUMAN	Disease (OBESITY)	13447331	A	S	127	L
14	UniProt	VAR_038644	R	165	Q	MC4R_HUMAN	Disease (OBESITY)	13447332	A	R	165	Q
15	UniProt	VAR_010709	R	165	W	MC4R_HUMAN	Disease (OBESITY)	13447332	A	R	165	W
16	UniProt	VAR_038645	I	170	V	MC4R_HUMAN	Disease (OBESITY)	121913560	A	I	170	V
17	UniProt	VAR_038646	A	175	T	MC4R_HUMAN	Disease (OBESITY)	121913563	A	A	175	T
18	UniProt	VAR_038647	G	181	D	MC4R_HUMAN	Disease (OBESITY)	13447333	A	G	181	D
19	UniProt	VAR_038648	A	219	V	MC4R_HUMAN	Disease (OBESITY)	121913567	A	A	219	V
20	UniProt	VAR_038649	I	226	T	MC4R_HUMAN	Polymorphism	193922686	A	I	226	T
21	UniProt	VAR_010710	I	251	L	MC4R_HUMAN	Polymorphism	52820871	A	I	251	L
22	UniProt	VAR_010711	G	252	S	MC4R_HUMAN	Disease (OBESITY)	13447336	A	G	252	S
23	UniProt	VAR_038650	V	253	I	MC4R_HUMAN	Disease (OBESITY)	187152753	A	V	253	I
24	UniProt	VAR_038651	C	271	R	MC4R_HUMAN	Disease (OBESITY)	---	A	C	271	R
25	UniProt	VAR_038652	C	271	Y	MC4R_HUMAN	Disease (OBESITY)	121913562	A	C	271	Y
26	UniProt	VAR_015357	N	274	S	MC4R_HUMAN	Disease (OBESITY)	121913561	A	N	274	S
27	UniProt	VAR_038653	I	316	S	MC4R_HUMAN	Disease (OBESITY)	121913564	A	I	316	S
28	UniProt	VAR_010712	I	317	T	MC4R_HUMAN	Disease (OBESITY)	13447337	A	I	317	T

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

Theoretical Model (3, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AGOUTI_1	PS60024	Agouti domain signature.	AGRP_HUMAN	87-129	1	B:87-129
2	AGOUTI_2	PS51150	Agouti domain profile.	AGRP_HUMAN	87-129	1	B:87-129
3	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	MC4R_HUMAN	135-151	1	A:135-151

Theoretical Model (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000290953	1	ENSE00001047346	chr16:67517716-67517420	297	AGRP_HUMAN	-	0	0	-	-
1.2	ENST00000290953	2	ENSE00001047348	chr16:67517304-67517172	133	AGRP_HUMAN	1-44	44	0	-	-
1.3	ENST00000290953	3	ENSE00001047349	chr16:67517013-67516928	86	AGRP_HUMAN	44-72	29	0	-	-
1.4b	ENST00000290953	4b	ENSE00001884910	chr16:67516721-67516474	248	AGRP_HUMAN	73-132	60	1	B:87-132	46

2.1	ENST00000299766	1	ENSE00001104613	chr18:58040001-58038564	1438	MC4R_HUMAN	1-472	472	1	A:40-321	282

Theoretical Model

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:282
 aligned with MC4R_HUMAN | P32245 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:282
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319  
           MC4R_HUMAN    40 CYEQLFVSPEVFVTLGVISLLENILVIVAIAKNKNLHSPMYFFICSLAVADMLVSVSNGSETIVITLLNSTDTDAQSFTVNIDNVIDSVICSSLLASICSLLSIAVDRYFTIFYALQYHNIMTVKRVGIIISCIWAACTVSGILFIIYSDSSAVIICLITMFFTMLALMASLYVHMFLMARLHIKRIAVLPGTGAIRQGANMKGAITLTILIGVFVVCWAPFFLHLIFYISCPQNPYCVCFMSHFNLYLILIMCNSIIDPLIYALRSQELRKTFKEIICCYP 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) ----------M-------C---S---------K-----L------------------D----SI--P-----M------------K-L-------------------------------------Q----V----T-----D-------------------------------------V------T------------------------LSI-----------------R--S-----------------------------------------ST---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------T--------------------------------------------------------------W---------------------------------------------------------------------------------------------------------Y-------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:40-321 UniProt: 1-472 [INCOMPLETE]                                                                                                                                                                                                                                        Transcript 2
                 2iqv A  40 CYEQLFVSPEVFVTLGVISLLENILVIVAIAKNKNLHSPMYFFICSLAVADMLVSVSNGSETIIITLLNSTDTDAQSFTVNIDNVIDSVICSSLLASICSLLSIAVDRYFTIFYALQYHNIMTVKRVGIIISCIWAACTVSGILFIIYSDSSAVIICLITMFFTMLALMASLYVHMFLMARLHIKRIAVLPGTGAIRQGANMKGAITLTILIGVFVVCWAPFFLHLIFYISCPQNPYCVCFMSHFNLYLILIMCNSIIDPLIYALRSQELRKTFKEIICCYP 321
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319

Chain B from PDB  Type:PROTEIN  Length:46
 aligned with AGRP_HUMAN | O00253 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:46
                                    96       106       116       126      
           AGRP_HUMAN    87 CVRLHESCLGQQVPCCDPCATCYCRFFNAFCYCRKLGTAMNPCSRT 132
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ....................eeee......eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                PROSITE (1) AGOUTI_1  PDB: B:87-129 UniProt: 87-129    --- PROSITE (1)
                PROSITE (2) AGOUTI_2  PDB: B:87-129 UniProt: 87-129    --- PROSITE (2)
               Transcript 1 Exon 1.4b  PDB: B:87-132 UniProt: 73-132       Transcript 1
                 2iqv B  87 CVRLHESCLGQQVPCCDPCATCYCRFFNAFCYCRKLGTAMNPCSRT 132
                                    96       106       116       126

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 2IQV)

(no "CATH Domain" information available for 2IQV)

(no "Pfam Domain" information available for 2IQV)

Theoretical Model(hide GO term definitions)

Chain A (MC4R_HUMAN | P32245)

molecular function
	GO:0004930	G-protein coupled receptor activity	Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
	GO:0004977	melanocortin receptor activity	Combining with melanocortin to initiate a change in cell activity.
	GO:0004980	melanocyte-stimulating hormone receptor activity	Combining with melanocyte-stimulating hormone to initiate a change in cell activity.
	GO:0042923	neuropeptide binding	Interacting selectively and non-covalently and stoichiometrically with neuropeptides, peptides with direct synaptic effects (peptide neurotransmitters) or indirect modulatory effects on the nervous system (peptide neuromodulators).
	GO:0017046	peptide hormone binding	Interacting selectively and non-covalently with any peptide with hormonal activity in animals.
	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:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
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:0002024	diet induced thermogenesis	The process that results in increased metabolic rate in tissues of an organism. It is triggered by the detection of dietary excess. This process is achieved via signalling in the sympathetic nervous system.
	GO:0006112	energy reserve metabolic process	The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
	GO:0007631	feeding behavior	Behavior associated with the intake of food.
	GO:0030073	insulin secretion	The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
	GO:2000252	negative regulation of feeding behavior	Any process that stops, prevents or reduces the frequency, rate or extent of feeding behavior.
	GO:0045780	positive regulation of bone resorption	Any process that activates or increases the frequency, rate or extent of bone resorption.
	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:0060259	regulation of feeding behavior	Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food.
	GO:2000821	regulation of grooming behavior	Any process that modulates the frequency, rate or extent of grooming behavior.
	GO:0019222	regulation of metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
	GO:0032868	response to insulin	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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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.

Chain B (AGRP_HUMAN | O00253)

molecular function
	GO:0005184	neuropeptide hormone activity	The action characteristic of a neuropeptide hormone, any peptide hormone that acts in the central nervous system. A neuropeptide is any of several types of molecules found in brain tissue, composed of short chains of amino acids; they include endorphins, enkephalins, vasopressin, and others. They are often localized in axon terminals at synapses and are classified as putative neurotransmitters, although some are also hormones.
	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:0008343	adult feeding behavior	Feeding behavior in a fully developed and mature organism.
	GO:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0042755	eating behavior	The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue.
	GO:0007631	feeding behavior	Behavior associated with the intake of food.
	GO:0009755	hormone-mediated signaling pathway	A series of molecular signals mediated by the detection of a hormone.
	GO:0060135	maternal process involved in female pregnancy	A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
	GO:0007218	neuropeptide signaling pathway	The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor.
	GO:0009648	photoperiodism	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a period of light or dark of a given length, measured relative to a particular duration known as the 'critical day length'. The critical day length varies between species.
	GO:2000253	positive regulation of feeding behavior	Any process that activates or increases the frequency, rate or extent of feeding behavior.
	GO:0060259	regulation of feeding behavior	Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food.
	GO:0032868	response to insulin	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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

Theoretical Model
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(no "Sites" information available for 2iqv)

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	MC4R_HUMAN \| P32245
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	AGRP_HUMAN \| O00253	:	1hyk 1mr0
	MC4R_HUMAN \| P32245	:	2iqp 2iqr 2iqs 2iqu 2iqw

(no "Related Entries Specified in the PDB File" available for 2IQV)

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (7, 7)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (28, 28)

PROSITE Motifs (3, 2)

Exons (2, 2)

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