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- PDB-4gjb: Crystal structure of renin in complex with NVP-BBV031 (compound 6) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gjb | ||||||
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Title | Crystal structure of renin in complex with NVP-BBV031 (compound 6) | ||||||
![]() | Renin![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ostermann, N. / Zink, F. / Kroemer, M. | ||||||
![]() | ![]() Title: A novel class of oral direct Renin inhibitors: highly potent 3,5-disubstituted piperidines bearing a tricyclic p3-p1 pharmacophore. Authors: Ostermann, N. / Ruedisser, S. / Ehrhardt, C. / Breitenstein, W. / Marzinzik, A. / Jacoby, E. / Vangrevelinghe, E. / Ottl, J. / Klumpp, M. / Hartwieg, J.C. / Cumin, F. / Hassiepen, U. / ...Authors: Ostermann, N. / Ruedisser, S. / Ehrhardt, C. / Breitenstein, W. / Marzinzik, A. / Jacoby, E. / Vangrevelinghe, E. / Ottl, J. / Klumpp, M. / Hartwieg, J.C. / Cumin, F. / Hassiepen, U. / Trappe, J. / Sedrani, R. / Geisse, S. / Gerhartz, B. / Richert, P. / Francotte, E. / Wagner, T. / Kromer, M. / Kosaka, T. / Webb, R.L. / Rigel, D.F. / Maibaum, J. / Baeschlin, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.9 KB | Display | ![]() |
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PDB format | ![]() | 114.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4gj8C ![]() 4gj9C ![]() 4gjaC ![]() 4gjcC ![]() 4gjdC ![]() 2v0zS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Sugar | ![]() #3: Chemical | #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.64 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: reservoir: 18-21% PEG4000, 0.4-0.6 M sodium chloride, 50 mM sodium citrate, pH 4-5, protein solution: 10-15 mg/mL protein, 25 mM sodium chloride, 12.5 mM Tris, pH 8, drop: 1 uL protein ...Details: reservoir: 18-21% PEG4000, 0.4-0.6 M sodium chloride, 50 mM sodium citrate, pH 4-5, protein solution: 10-15 mg/mL protein, 25 mM sodium chloride, 12.5 mM Tris, pH 8, drop: 1 uL protein solution + 1 uL reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 5, 2004 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.75→59.9 Å / Num. obs: 25378 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 69.82 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.75→2.85 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.9 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2V0Z Resolution: 2.75→59.42 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.8809 / SU R Cruickshank DPI: 0.607 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.684 / SU Rfree Blow DPI: 0.297 / SU Rfree Cruickshank DPI: 0.297 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 54.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.318 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→59.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.86 Å / Total num. of bins used: 13
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