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Yorodumi- PDB-5uov: HIV-1 wild Type protease with GRL-1118A , an isophthalamide-deriv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uov | |||||||||||||||||||||||||||
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Title | HIV-1 wild Type protease with GRL-1118A , an isophthalamide-derived P2-P3 ligand with the sulfonamide isostere as the P2' group | |||||||||||||||||||||||||||
Components | Protease | |||||||||||||||||||||||||||
Keywords | hydrolase/hydrolase inhibitor / an isophthalamide-derived P2-P3 ligand / HIV-1 protease inhibitor GRL-1118A / darunavir / multidrug-resistant / hydrolase inhibitor complex / hydrolase-hydrolase inhibitor complex | |||||||||||||||||||||||||||
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: 1.33 Å | |||||||||||||||||||||||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | |||||||||||||||||||||||||||
Funding support | United States, Japan, 8items
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Citation | Journal: Bioorg. Med. Chem. / Year: 2017 Title: Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex. Authors: Ghosh, A.K. / Brindisi, M. / Nyalapatla, P.R. / Takayama, J. / Ella-Menye, J.R. / Yashchuk, S. / Agniswamy, J. / Wang, Y.F. / Aoki, M. / Amano, M. / Weber, I.T. / Mitsuya, H. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uov.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uov.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 5uov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/5uov ftp://data.pdbj.org/pub/pdb/validation_reports/uo/5uov | HTTPS FTP |
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-Related structure data
Related structure data | 5upzC 3djkS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: C8B467, UniProt: P03366*PLUS |
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-Non-polymers , 6 types, 179 molecules
#2: Chemical | ChemComp-8FP / | ||||||
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#3: Chemical | ChemComp-NA / | ||||||
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-ACT / | #7: 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: 54.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.28 M NaCl, 0.1 M Sodium Acetate, pH 4.8 / PH range: 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→50 Å / Num. obs: 52049 / % possible obs: 96.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.33→1.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.2 / % possible all: 72.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DJK Resolution: 1.33→50 Å / Num. parameters: 16582 / Num. restraintsaints: 21576 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 38 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1706.85 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→50 Å
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Refine LS restraints |
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