+Open data
-Basic information
Entry | Database: PDB / ID: 3vsw | ||||||
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Title | Human renin in complex with compound 8 | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / RAS / hypertension / inhibitor / Aspartyl protease / 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 / amyloid-beta metabolic process ...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 / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / hormone-mediated signaling pathway / kidney development / insulin-like growth factor receptor binding / 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: 3 Å | ||||||
Authors | Takahashi, M. / Hanzawa, H. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Design and optimization of novel (2S,4S,5S)-5-amino-6-(2,2-dimethyl-5-oxo-4-phenylpiperazin-1-yl)-4-hydroxy-2-isopropylhexanamides as renin inhibitors Authors: Nakamura, Y. / Sugita, C. / Meguro, M. / Miyazaki, S. / Tamaki, K. / Takahashi, M. / Nagai, Y. / Nagayama, T. / Kato, M. / Suemune, H. / Nishi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vsw.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vsw.ent.gz | 112.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vsw_validation.pdf.gz | 983.5 KB | Display | wwPDB validaton report |
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Full document | 3vsw_full_validation.pdf.gz | 1010.4 KB | Display | |
Data in XML | 3vsw_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 3vsw_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/3vsw ftp://data.pdbj.org/pub/pdb/validation_reports/vs/3vsw | HTTPS FTP |
-Related structure data
Related structure data | 3vsxC 1rneS 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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5 |
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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 | |
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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: 3.12 Å3/Da / Density % sol: 60.56 % / Mosaicity: 0.827 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3 Details: 5-12% PEG 3350, 0.6M NaCl, 0.1M citrate (pH3.0-4.5), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 14, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 18881 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.053 / Χ2: 1.677 / Net I/σ(I): 28.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RNE Resolution: 3→19.91 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7332 / Data cutoff high absF: 1661881 / 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: 15.618 Å2 / ksol: 0.3285 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.75 Å2 / Biso mean: 29.8287 Å2 / Biso min: 8.18 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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