+Open data
-Basic information
Entry | Database: PDB / ID: 2iku | ||||||
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Title | Crystal Structure of Human Renin Complexed with Inhibitors | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE / Renin / Inhibitors / Drug Design | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Mochalkin, I. | ||||||
Citation | Journal: Anal.Biochem. / Year: 2007 Title: Binding thermodynamics of substituted diaminopyrimidine renin inhibitors. Authors: Sarver, R.W. / Peevers, J. / Cody, W.L. / Ciske, F.L. / Dyer, J. / Emerson, S.D. / Hagadorn, J.C. / Holsworth, D.D. / Jalaie, M. / Kaufman, M. / Mastronardi, M. / McConnell, P. / Powell, N.A. ...Authors: Sarver, R.W. / Peevers, J. / Cody, W.L. / Ciske, F.L. / Dyer, J. / Emerson, S.D. / Hagadorn, J.C. / Holsworth, D.D. / Jalaie, M. / Kaufman, M. / Mastronardi, M. / McConnell, P. / Powell, N.A. / Quin, J. / Van Huis, C.A. / Zhang, E. / Mochalkin, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iku.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iku.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 2iku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iku_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2iku_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2iku_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 2iku_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/2iku ftp://data.pdbj.org/pub/pdb/validation_reports/ik/2iku | HTTPS FTP |
-Related structure data
Related structure data | 2ikoSC 2il2C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00797, renin #2: Chemical | #3: 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: 3.14 Å3/Da / Density % sol: 60.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 10-20% PEG 3350, 50 mM sodium citrate pH 4.5, 0.6 M NaCl., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 28798 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.125 / Χ2: 1.143 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.08 / Num. unique all: 2858 / Χ2: 0.667 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IKO Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 20.616 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.547 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.948 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.598→2.664 Å / Total num. of bins used: 20
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