+Open data
-Basic information
Entry | Database: PDB / ID: 4pyv | ||||||
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Title | Crystal structure of renin in complex with compound4 | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Renin inhibitor / 3 / 5-substituted piperidines / HYDROLASE INHIBITOR COMPLEX / Hydrolase / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å | ||||||
Authors | Ostermann, N. / Zink, F. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2014 Title: Structure-based design of substituted piperidines as a new class of highly efficacious oral direct Renin inhibitors. Authors: Ehara, T. / Irie, O. / Kosaka, T. / Kanazawa, T. / Breitenstein, W. / Grosche, P. / Ostermann, N. / Suzuki, M. / Kawakami, S. / Konishi, K. / Hitomi, Y. / Toyao, A. / Gunji, H. / Cumin, F. / ...Authors: Ehara, T. / Irie, O. / Kosaka, T. / Kanazawa, T. / Breitenstein, W. / Grosche, P. / Ostermann, N. / Suzuki, M. / Kawakami, S. / Konishi, K. / Hitomi, Y. / Toyao, A. / Gunji, H. / Cumin, F. / Schiering, N. / Wagner, T. / Rigel, D.F. / Webb, R.L. / Maibaum, J. / Yokokawa, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pyv.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pyv.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/4pyv ftp://data.pdbj.org/pub/pdb/validation_reports/py/4pyv | 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
-Protein / Sugars , 2 types, 3 molecules AB
#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) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHINESE HAMSTER / References: UniProt: P00797, renin #2: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 144 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: 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: 3.19 Å3/Da / Density % sol: 61.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: REMARK: HANGING DROP, VAPOR DIFFUSION, 20 DEG C, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 31.7 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 18% PEG4000, 50 MM ...Details: REMARK: HANGING DROP, VAPOR DIFFUSION, 20 DEG C, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 31.7 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 18% PEG4000, 50 MM NACITRATE PH 4.5, 400 MM NACL; SOAKING: DROP PLUS 2.5 UL RESERVOIR SOLUTION PLUS 10 MM INHIBITOR AND 10% DMSO FOR 30 MIN; CRYO: SOAKING SOLUTION PLUS 15% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97933 / Wavelength: 0.979334 Å | |||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 23, 2004 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.65→42.78 Å / Num. all: 27773 / Num. obs: 27773 / % possible obs: 99.45 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 79.68 Å2 | |||||||||
Reflection shell | Resolution: 2.65→2.75 Å / % possible all: 99.45 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.65→42.78 Å / Cor.coef. Fo:Fc: 0.9431 / Cor.coef. Fo:Fc free: 0.9184 / SU R Cruickshank DPI: 0.492 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 66.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.359 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→42.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.75 Å / Total num. of bins used: 14
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