[English] 日本語
Yorodumi- PDB-4gjb: Crystal structure of renin in complex with NVP-BBV031 (compound 6) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gjb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of renin in complex with NVP-BBV031 (compound 6) | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / renin inhibitor / fragment based screening / 3 / 5-disubstituted piperidines / 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 / cell maturation / response to immobilization stress / 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 / cell maturation / response to immobilization stress / amyloid-beta metabolic process / hormone-mediated signaling pathway / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / response to cAMP / insulin-like growth factor receptor binding / kidney development / regulation of blood pressure / cellular response to xenobiotic stimulus / male gonad development / apical part of cell / peptidase activity / aspartic-type endopeptidase activity / response to lipopolysaccharide / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Ostermann, N. / Zink, F. / Kroemer, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4gjb.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4gjb.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gjb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4gjb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4gjb_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 4gjb_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/4gjb ftp://data.pdbj.org/pub/pdb/validation_reports/gj/4gjb | HTTPS FTP |
-Related structure data
Related structure data | 4gj8C 4gj9C 4gjaC 4gjcC 4gjdC 2v0zS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00797, renin #2: Sugar | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.64 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00027 Å |
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: 1.00027 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.54 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.318 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→59.42 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.86 Å / Total num. of bins used: 13
|