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Yorodumi- PDB-2joa: HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2joa | ||||||
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Title | HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances | ||||||
Components |
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Keywords | PROTEIN BINDING / PDZ / beta-sandwich / cyclically-permuted | ||||||
Function / homology | Function and homology information chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development ...chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development / collagen-containing extracellular matrix / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Runyon, S.T. / Zhang, Y. / Appleton, B.A. / Sazinksy, S.L. / Wu, P. / Pan, B. / Wiesmann, C. / Skelton, N.J. / Sidhu, S.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3 Authors: Runyon, S.T. / Zhang, Y. / Appleton, B.A. / Sazinsky, S.L. / Wu, P. / Pan, B. / Wiesmann, C. / Skelton, N.J. / Sidhu, S.S. #1: Journal: To be Published Title: HtrA1 bound to an optimized peptide: NMR assignment of PDZ domain and ligand resonances Authors: Runyon, S.T. / Pan, B. / Skelton, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2joa.cif.gz | 694.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2joa.ent.gz | 580.3 KB | Display | PDB format |
PDBx/mmJSON format | 2joa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2joa_validation.pdf.gz | 488.9 KB | Display | wwPDB validaton report |
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Full document | 2joa_full_validation.pdf.gz | 741.4 KB | Display | |
Data in XML | 2joa_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 2joa_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/2joa ftp://data.pdbj.org/pub/pdb/validation_reports/jo/2joa | HTTPS FTP |
-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: 11582.238 Da / Num. of mol.: 1 / Fragment: PDZ domain, residues 379-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein/peptide | Mass: 962.083 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The peptide was derived from a phage-displayed library as an optimal ligand for binding to the PDZ domain of human HtrA1. Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.025 / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 / Details: followed by cartesian dynamics and minimization | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1352 / NOE intraresidue total count: 179 / NOE long range total count: 504 / NOE medium range total count: 252 / NOE sequential total count: 340 / Hydrogen bond constraints total count: 42 / Protein chi angle constraints total count: 21 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 77 / Protein psi angle constraints total count: 76 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.9 ° / Maximum upper distance constraint violation: 0.08 Å / Torsion angle constraint violation method: CNX | ||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0049 Å / Distance rms dev error: 0.0008 Å |