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Yorodumi- PDB-4cod: Encoded library technology as a source of hits for the discovery ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cod | ||||||
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Title | Encoded library technology as a source of hits for the discovery and lead optimization of a potent and selective class of bactericidal direct inhibitors of Mycobacterium tuberculosis InhA | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
Keywords | TRANSFERASE / ELT / ENCODED LIBRARY TECHNOLOGY / ISONIAZID / L-PROLINE | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Encinas, L. / OKeefe, H. / Neu, M. / Convery, M.A. / McDowell, W. / Mendoza-Losana, A. / Pages, L.B. / Castro-Pichel, J. / Evindar, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Encoded Library Technology as a Source of Hits for the Discovery and Lead Optimization of a Potent and Selective Class of Bactericidal Direct Inhibitors of Mycobacterium Tuberculosis Inha. Authors: Encinas, L. / O'Keefe, H. / Neu, M. / Remuinan, M.J. / Patel, A.M. / Guardia, A. / Davie, C.P. / Perez-Macias, N. / Yang, H. / Convery, M.A. / Messer, J.A. / Perez-Herran, E. / Centrella, P. ...Authors: Encinas, L. / O'Keefe, H. / Neu, M. / Remuinan, M.J. / Patel, A.M. / Guardia, A. / Davie, C.P. / Perez-Macias, N. / Yang, H. / Convery, M.A. / Messer, J.A. / Perez-Herran, E. / Centrella, P.A. / Alvarez-Gomez, D. / Clark, M.A. / Huss, S. / O'Donovan, G.K. / Ortega-Muro, F. / Mcdowell, W. / Castaneda, P. / Arico-Muendel, C.C. / Pajk, S. / Rullas, J. / Angulo-Barturen, I. / Alvarez-Ruiz, E. / Mendoza-Losana, A. / Pages, L.B. / Castro-Pichel, J. / Evindar, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cod.cif.gz | 427.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cod.ent.gz | 359.9 KB | Display | PDB format |
PDBx/mmJSON format | 4cod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cod_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 4cod_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 4cod_validation.xml.gz | 44.7 KB | Display | |
Data in CIF | 4cod_validation.cif.gz | 60.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4cod ftp://data.pdbj.org/pub/pdb/validation_reports/co/4cod | HTTPS FTP |
-Related structure data
Related structure data | 2h7i S: Starting model for refinement |
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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: 28554.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-KV1 / #3: Chemical | ChemComp-NAD / #4: 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: 4.03 Å3/Da / Density % sol: 69.44 % Description: RMERG FOR HIGH RESOLUTION SHELL IS 1.977. DATA IS VERY ANISOTROPIC. DATA USED IN REFINEMENT HAS BEEN TRUNCATED TO 3.2A IN THE A* DIRECTION |
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Crystal grow | pH: 8.5 Details: 10% PEG 8K, 0.1M TRIS PH8.5 25% ETHYLENE GLYCOL USED AS CRYO. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→102.6 Å / Num. obs: 72859 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 71.11 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H7I 2h7i Resolution: 2.4→35.14 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.226
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Displacement parameters | Biso mean: 62.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.337 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→35.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 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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