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Yorodumi- PDB-3o3z: Complex of a chimeric alpha/beta-peptide based on the gp41 CHR do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o3z | |||||||||
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Title | Complex of a chimeric alpha/beta-peptide based on the gp41 CHR domain bound to a gp41 NHR domain peptide | |||||||||
Components |
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Keywords | VIRAL PROTEIN / HIV fusion inhibitor / mixed alpha-peptide/beta-peptide backbone | |||||||||
Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Horne, W.S. / Johnson, L.M. / Gellman, S.H. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Broad Distribution of Energetically Important Contacts across an Extended Protein Interface. Authors: Johnson, L.M. / Horne, W.S. / Gellman, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o3z.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o3z.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 3o3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o3z_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 3o3z_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 3o3z_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 3o3z_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o3z ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o3z | HTTPS FTP |
-Related structure data
Related structure data | 3o3xC 3o40C 3o43C 3f50S C: citing same article (ref.) 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/peptide | Mass: 4150.851 Da / Num. of mol.: 1 / Fragment: UNP residues 554 to 589 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q9YP39 | ||
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#2: Protein/peptide | Mass: 4503.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide | ||
#3: Chemical | #4: 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: 3.04 Å3/Da / Density % sol: 59.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.17 M NaOAc, 0.085 M Tris pH 8.5, 25% w/v PEG 4000, 15% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2008 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 3662 / % possible obs: 99.8 % / Redundancy: 39 % / Rsym value: 0.077 / Net I/σ(I): 74.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F50 Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.862 / SU B: 10.795 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R Free: 0.32 / 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: 43.432 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.672 Å / Total num. of bins used: 20
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