+Open data
-Basic information
Entry | Database: PDB / ID: 6vgc | ||||||
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Title | Crystal Structures of FLAP bound to DG-031 | ||||||
Components | 5-lipoxygenase-activating protein | ||||||
Keywords | MEMBRANE PROTEIN / 5-Lipoxygenase Activating Protein / FLAP / DG-031 | ||||||
Function / homology | Function and homology information leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / Synthesis of Leukotrienes (LT) and Eoxins (EX) / positive regulation of acute inflammatory response / leukotriene biosynthetic process / glutathione peroxidase activity ...leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / Synthesis of Leukotrienes (LT) and Eoxins (EX) / positive regulation of acute inflammatory response / leukotriene biosynthetic process / glutathione peroxidase activity / arachidonic acid binding / protein homotrimerization / glutathione transferase activity / enzyme activator activity / cellular response to calcium ion / nuclear envelope / nuclear membrane / protein-containing complex binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Ho, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. ...Ho, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. / Hickey, M.J. / Hughes, N.E. / Chandrasekhar, S. / Sloan, A.V. / Gooding, K. / Harvey, A. / Yu, X.P. / Kahl, S.D. / Norman, B.H. | ||||||
Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2020 Title: Structure-based, multi-targeted drug discovery approach to eicosanoid inhibition: Dual inhibitors of mPGES-1 and 5-lipoxygenase activating protein (FLAP). Authors: Ho, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. / Hickey, M.J. / Hughes, N.E. / Chandrasekhar, S. / Sloan, ...Authors: Ho, J.D. / Lee, M.R. / Rauch, C.T. / Aznavour, K. / Park, J.S. / Luz, J.G. / Antonysamy, S. / Condon, B. / Maletic, M. / Zhang, A. / Hickey, M.J. / Hughes, N.E. / Chandrasekhar, S. / Sloan, A.V. / Gooding, K. / Harvey, A. / Yu, X.P. / Kahl, S.D. / Norman, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vgc.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vgc.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vgc_validation.pdf.gz | 571.5 KB | Display | wwPDB validaton report |
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Full document | 6vgc_full_validation.pdf.gz | 573.5 KB | Display | |
Data in XML | 6vgc_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 6vgc_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/6vgc ftp://data.pdbj.org/pub/pdb/validation_reports/vg/6vgc | HTTPS FTP |
-Related structure data
Related structure data | 6vgiC 6vl4C 2q7mS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19327.193 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX5AP, FLAP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20292 #2: Chemical | ChemComp-QY1 / ( #3: Chemical | #4: Sugar | ChemComp-BOG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.18 Å3/Da / Density % sol: 61.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 100 mM MES pH 6.5, 26% PEG 350 MME, 200 mM Calcium Chloride, 1 mM DG-031 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→101.49 Å / Num. obs: 54437 / % possible obs: 98 % / Redundancy: 3.8 % / Rsym value: 0.042 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.37→2.5 Å / Num. unique obs: 3982 / Rsym value: 0.4 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q7M Resolution: 2.37→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.697 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.255 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.48 Å2 / Biso mean: 57.442 Å2 / Biso min: 12.44 Å2
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Refinement step | Cycle: final / Resolution: 2.37→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.374→2.435 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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