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Yorodumi- PDB-1y7k: NMR structure family of Human Agouti Signalling Protein (80-132: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y7k | ||||||
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Title | NMR structure family of Human Agouti Signalling Protein (80-132: Q115Y, S124Y) | ||||||
Components | Agouti Signaling ProteinAgouti-signaling protein | ||||||
Keywords | SIGNALING PROTEIN / Melanocortin / inhibitor / cystine knot / GPCR / endogenous antagonist / inverse agonist | ||||||
Function / homology | Function and homology information melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / adult feeding behavior / positive regulation of melanin biosynthetic process / melanosome transport / melanin biosynthetic process / melanosome organization / neuropeptide hormone activity / epigenetic programming in the zygotic pronuclei ...melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / adult feeding behavior / positive regulation of melanin biosynthetic process / melanosome transport / melanin biosynthetic process / melanosome organization / neuropeptide hormone activity / epigenetic programming in the zygotic pronuclei / hormone-mediated signaling pathway / generation of precursor metabolites and energy / cell-cell signaling / signaling receptor binding / signal transduction / extracellular space Similarity search - Function | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model type details | minimized average | ||||||
Authors | McNulty, J.C. / Jackson, P.J. / Thompson, D.A. / Chai, B. / Gantz, I. / Barsh, G.S. / Dawson, P.E. / Millhauser, G.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structures of the agouti signaling protein. Authors: McNulty, J.C. / Jackson, P.J. / Thompson, D.A. / Chai, B. / Gantz, I. / Barsh, G.S. / Dawson, P.E. / Millhauser, G.L. #1: Journal: Biochemistry / Year: 2001 Title: High-resolution NMR structure of the chemically-synthesized melanocortin receptor binding domain AGRP(87-132) of the agouti-related protein Authors: McNulty, J.C. / Thompson, D.A. / Bolin, K.A. / Wilken, J. / Barsh, G.S. / Millhauser, G.L. #2: Journal: Biochemistry / Year: 2002 Title: Design, pharmacology, and NMR structure of a minimized cystine knot with agouti-related protein activity Authors: Jackson, P.J. / McNulty, J.C. / Yang, Y.K. / Thompson, D.A. / Chai, B. / Gantz, I. / Barsh, G.S. / Millhauser, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y7k.cif.gz | 237.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y7k.ent.gz | 203.6 KB | Display | PDB format |
PDBx/mmJSON format | 1y7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y7k ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y7k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5823.997 Da / Num. of mol.: 1 / Fragment: residies 80-132 / Mutation: Q115Y, S124Y / Source method: obtained synthetically Details: Sequence occurs naturally in humans, genes ASIP, AGTI, AGTIL, ASP References: UniProt: P42127 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques, in conjunction with a semi-automated assignment protocol. |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: This structure family represents one of two major conformers present in solution. The two conformers arise from the cis-trans proline isomerization of the Ala104-Pro105 peptide bond. | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 21 Distance constraint violation method: From the original family of twenty, the representative conformer had the lowest target function and was subjected to further minimization in water. The remaining ...Distance constraint violation method: From the original family of twenty, the representative conformer had the lowest target function and was subjected to further minimization in water. The remaining structures were obtained without explicit inclusion of solvent. |