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Yorodumi- PDB-5t4s: Novel Approach of Fragment-Based Lead Discovery applied to Renin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t4s | ||||||
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Title | Novel Approach of Fragment-Based Lead Discovery applied to Renin Inhibitors | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / protein-ligand complex / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 Å | ||||||
Authors | Snell, G.P. / Behnke, C.A. / Okada, K. / Oki, H. / Sang, B.C. / Lane, W. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2016 Title: Novel approach of fragment-based lead discovery applied to renin inhibitors. Authors: Tawada, M. / Suzuki, S. / Imaeda, Y. / Oki, H. / Snell, G. / Behnke, C.A. / Kondo, M. / Tarui, N. / Tanaka, T. / Kuroita, T. / Tomimoto, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t4s.cif.gz | 266.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t4s.ent.gz | 219.2 KB | Display | PDB format |
PDBx/mmJSON format | 5t4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/5t4s ftp://data.pdbj.org/pub/pdb/validation_reports/t4/5t4s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 37153.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P00797, renin #2: Sugar | |
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-Non-polymers , 5 types, 146 molecules
#3: Chemical | ChemComp-PG6 / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-77O / | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.97 % / Mosaicity: 0.764 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 26% PEG600, 0.06M citrate, 0.04M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 6, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→50 Å / Num. obs: 27163 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.073 / Χ2: 1.083 / Net I/av σ(I): 19.397 / Net I/σ(I): 13.5 / Num. measured all: 135521 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 23.464 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.601 / ESU R Free: 0.316 / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.46 Å2 / Biso mean: 60.785 Å2 / Biso min: 35.25 Å2
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Refinement step | Cycle: final / Resolution: 2.64→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.638→2.706 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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