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Yorodumi- PDB-6bmz: Influenza A M2 transmembrane domain bound to a spiroadamantane in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bmz | ||||||
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Title | Influenza A M2 transmembrane domain bound to a spiroadamantane inhibitor | ||||||
Components | Matrix protein 2 | ||||||
Keywords | MEMBRANE PROTEIN / influenza M2 / proton channel / spiroadamantane | ||||||
Function / homology | Function and homology information suppression by virus of host autophagy / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.634 Å | ||||||
Authors | Thomaston, J.L. / DeGrado, W.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters. Authors: Thomaston, J.L. / Polizzi, N.F. / Konstantinidi, A. / Wang, J. / Kolocouris, A. / DeGrado, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bmz.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bmz.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bmz_validation.pdf.gz | 522.9 KB | Display | wwPDB validaton report |
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Full document | 6bmz_full_validation.pdf.gz | 524.8 KB | Display | |
Data in XML | 6bmz_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 6bmz_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/6bmz ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bmz | HTTPS FTP |
-Related structure data
Related structure data | 6bkkC 6bklC 6bocC 3lbwS 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2754.340 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q20MD5, UniProt: Q9Q0L9*PLUS #2: Chemical | ChemComp-E01 / ( #3: Chemical | ChemComp-CL / #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: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 0.1 M HEPES pH 7, 30% v/v PEG 400, monoolein, spiroadamantane amine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→72.59 Å / Num. obs: 11007 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.164 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.63→2.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 3 / Num. unique obs: 1442 / CC1/2: 0.92 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LBW Resolution: 2.634→58.591 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.634→58.591 Å
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Refine LS restraints |
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LS refinement shell |
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