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Yorodumi- PDB-2qd6: HIV-1 Protease Mutant I50V with potent Antiviral inhibitor GRL-98065 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qd6 | ||||||
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Title | HIV-1 Protease Mutant I50V with potent Antiviral inhibitor GRL-98065 | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE / HIV-1 protease mutant I50V / protease inhibitor | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Wang, Y.F. / Tie, Y. / Boross, P.I. / Tozser, J. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease. Authors: Wang, Y.F. / Tie, Y. / Boross, P.I. / Tozser, J. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qd6.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qd6.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 2qd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qd6 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qd6 | HTTPS FTP |
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-Related structure data
Related structure data | 2qciC 2qd7C 2qd8C 2z4oSC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10726.649 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A, I50V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03367, HIV-1 retropepsin |
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-Non-polymers , 5 types, 156 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-065 / ( | #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: 2.69 Å3/Da / Density % sol: 54.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25mM sodium acetate, 9.4% (w/v) sodium chloride, 6.7% (v/v) dimethylsulfoxide (DMSO), pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 / Wavelength: 1 Å | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2003 | |||||||||
Radiation | Monochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.28→50 Å / Num. all: 61481 / Num. obs: 60638 / % possible obs: 89.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.9 | |||||||||
Reflection shell | Resolution: 1.28→1.33 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.21 / Num. unique all: 3547 / % possible all: 59.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z4O Resolution: 1.28→10 Å / Num. parameters: 17186 / Num. restraintsaints: 23354 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 33 / Occupancy sum hydrogen: 1626.74 / Occupancy sum non hydrogen: 1686.34 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→10 Å
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Refine LS restraints |
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