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Yorodumi- PDB-2r5d: Structure of the gp41 N-trimer in complex with the HIV entry inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r5d | ||||||
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Title | Structure of the gp41 N-trimer in complex with the HIV entry inhibitor PIE7 | ||||||
Components |
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Keywords | VIRAL PROTEIN/inhibitor / HIV / viral entry / PIE / VIRAL PROTEIN-inhibitor complex | ||||||
Function / homology | Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / HIV ENTRY INHIBITOR PIE7 / polypeptide(D) / polypeptide(D) (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.66 Å | ||||||
Authors | VanDemark, A.P. / Welch, B. / Heroux, A. / Hill, C.P. / Kay, M.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Potent D-peptide inhibitors of HIV-1 entry Authors: Welch, B.D. / Vandemark, A.P. / Heroux, A. / Hill, C.P. / Kay, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r5d.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r5d.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 2r5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r5d_validation.pdf.gz | 483.7 KB | Display | wwPDB validaton report |
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Full document | 2r5d_full_validation.pdf.gz | 484.7 KB | Display | |
Data in XML | 2r5d_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2r5d_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/2r5d ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r5d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide / Polypeptide(D) , 2 types, 6 molecules ABCHKL
#1: Protein/peptide | Mass: 5466.574 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others) #2: Polypeptide(D) | |
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-Non-polymers , 4 types, 189 molecules
#3: Chemical | ChemComp-GOL / |
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#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-EPE / |
#6: 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: 2.46 Å3/Da / Density % sol: 49.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES, 24% PEG 10000, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 4, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.66→50 Å / Num. all: 24829 / Num. obs: 23406 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.046 / Χ2: 1.625 / Net I/σ(I): 21.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.66→38.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.434 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.122 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.427 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→38.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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