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Yorodumi- PDB-6o48: Wild-type HIV-1 protease in complex with a substrate analog CA-p2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o48 | ||||||
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Title | Wild-type HIV-1 protease in complex with a substrate analog CA-p2 | ||||||
Components | HIV-1 protease | ||||||
Keywords | HYDROLASE / VIRAL PROTEIN / HIV PROTEASE | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Wang, Y.-F. / Liu, F. / Weber, I.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Omega / Year: 2019 Title: Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues. Authors: Agniswamy, J. / Kneller, D.W. / Brothers, R. / Wang, Y.F. / 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 | 6o48.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o48.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o48_validation.pdf.gz | 698.4 KB | Display | wwPDB validaton report |
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Full document | 6o48_full_validation.pdf.gz | 701.5 KB | Display | |
Data in XML | 6o48_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6o48_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/6o48 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/6o48 | HTTPS FTP |
-Related structure data
Related structure data | 6o54C 6o57C 6o5aC 6o5xC 2aodS 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5RZ08, UniProt: P03366*PLUS |
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-Non-polymers , 6 types, 114 molecules
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-FMT / | #5: Chemical | ChemComp-0Q4 / | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H70N11O8 References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide #6: Chemical | ChemComp-GOL / | #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: 2.73 Å3/Da / Density % sol: 54.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1M sodium chloride and 0.1M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. obs: 38064 / % possible obs: 91.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / Num. unique obs: 2696 / % possible all: 66.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AOD Resolution: 1.46→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 19 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1680.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→50 Å
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Refine LS restraints |
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