+Open data
-Basic information
Entry | Database: PDB / ID: 3vye | ||||||
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Title | Human renin in complex with inhibitor 7 | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Aspartyl protease / RAS / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Takahashi, M. / Matsui, Y. / Hanzawa, H. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Design and discovery of new (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]piperidine-3-carboxamides as potent renin inhibitors Authors: Mori, Y. / Ogawa, Y. / Mochizuki, A. / Nakamura, Y. / Sugita, C. / Miyazaki, S. / Tamaki, K. / Matsui, Y. / Takahashi, M. / Nagayama, T. / Nagai, Y. / Inoue, S. / Nishi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vye.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vye.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vye ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vye | HTTPS FTP |
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-Related structure data
Related structure data | 3vydC 3vyfC 3vswS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37267.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Plasmid: pcDNA3.1 / Cell line (production host): 293F / 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: 3.16 Å3/Da / Density % sol: 61.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 5-12% PEG 3350, 0.6M NaCl, 0.1M citrate pH3.0-4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K PH range: 3.0-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.502 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.502 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 26105 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 67.7 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VSW Resolution: 2.7→19.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1563123.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7872 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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