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Yorodumi- PDB-3oot: Crystal Structure Analysis of Renin-indole-piperazin inhibitor co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oot | ||||||
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Title | Crystal Structure Analysis of Renin-indole-piperazin inhibitor complexes | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE / RENIN HUMAN / ASPARTYL PROTEASE / RENIN INHIBITION / HYPERTENSION | ||||||
Function / homology | Function and homology information renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / amyloid-beta metabolic process / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / kidney development / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.55 Å | ||||||
Authors | Bocskei, Z. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Discovery and optimization of a new class of potent and non-chiral indole-3-carboxamide-based renin inhibitors. Authors: Scheiper, B. / Matter, H. / Steinhagen, H. / Stilz, U. / Bocskei, Z. / Fleury, V. / McCort, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oot.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oot.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/3oot ftp://data.pdbj.org/pub/pdb/validation_reports/oo/3oot | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37267.008 Da / Num. of mol.: 2 / Fragment: unp residues 67-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REN Cell line (production host): HUMAN EMBRYONIC KIDNEY CELL (CRL-1573) Production host: HOMO SAPIENS (human) / References: UniProt: P00797, renin #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.05M CITRATE PH=4.5, 10-12% PEG3350, 0.6M NACL, 20 MG/ML RENIN, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 293 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 23, 2006 / Details: Osmic blue mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→50 Å / Num. obs: 31582 / % possible obs: 97.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.102 / Χ2: 1.128 / Net I/σ(I): 9.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.55→33.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9275 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: POSITION OF WATER MOLECULES WERE TAKEN FROM A HIGHER RESOLUTION STRUCTURE (2.05 A). WATERS WERE REFINED AND RETAINED ONLY IF THE ISOTROPIC DISPLACEMENT PARAMETER REMAINED BELOW 80 A**2
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Displacement parameters | Biso max: 144.74 Å2 / Biso mean: 54.0084 Å2 / Biso min: 25.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.314 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→33.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.63 Å / Total num. of bins used: 16
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