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Yorodumi- PDB-4gzf: Multi-drug resistant HIV-1 protease 769 variant with reduced LrF ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gzf | ||||||||||||
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Title | Multi-drug resistant HIV-1 protease 769 variant with reduced LrF peptide | ||||||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Multi-drug resistance / Protease inhibitor / Drug resistance / substrate peptides / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Human immunodeficiency virus 1 synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||||||||
Authors | Dewdney, T.G. / Wang, Y. / Kovari, I.A. / Brunzelle, J.S. / Reiter, S.J. / Kovari, L.C. | ||||||||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2013 Title: Ligand modifications to reduce the relative resistance of multi-drug resistant HIV-1 protease. Authors: Dewdney, T.G. / Wang, Y. / Liu, Z. / Sharma, S.K. / Reiter, S.J. / Brunzelle, J.S. / Kovari, I.A. / Woster, P.M. / Kovari, L.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gzf.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gzf.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gzf_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
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Full document | 4gzf_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 4gzf_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4gzf_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/4gzf ftp://data.pdbj.org/pub/pdb/validation_reports/gz/4gzf | HTTPS FTP |
-Related structure data
Related structure data | 4gyeC 3so9S 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 | Mass: 10770.686 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-99 / Mutation: Q7K, D25N, M36V, A82T, I84V Source method: isolated from a genetically manipulated source Details: The sequence is a clinical isolate with mutations introduced Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RTL1, UniProt: Q9QM22*PLUS #2: Protein/peptide | | Type: Peptide-like / Class: Inhibitor / Mass: 834.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-[(2S)-2-({N~5~-[(1E)-ethanimidoyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucine #3: 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: 2.1 Å3/Da / Density % sol: 41.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M citric acid and 2.4 M ammonium sulfate at pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 |
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Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 10, 2012 |
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.053→42.02 Å / Num. obs: 11642 |
Reflection shell | Resolution: 2.05→2.16 Å / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SO9 Resolution: 2.05→42.02 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.486 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.217 / 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: 20.649 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→42.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.053→2.106 Å / Total num. of bins used: 20
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