+Open data
-Basic information
Entry | Database: PDB / ID: 4q5m | ||||||
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Title | D30N tethered HIV-1 protease dimer/saquinavir complex | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.795 Å | ||||||
Authors | Prashar, V. / Bihani, S.C. / Ferrer, J.L. / Hosur, M.V. | ||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2015 Title: Structural Basis of Why Nelfinavir-Resistant D30N Mutant of HIV-1 Protease Remains Susceptible to Saquinavir. Authors: Prashar, V. / Bihani, S.C. / Ferrer, J.L. / Hosur, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q5m.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q5m.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 4q5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q5m_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4q5m_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4q5m_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 4q5m_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/4q5m ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q5m | HTTPS FTP |
-Related structure data
Related structure data | 1lv1S 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: 21900.789 Da / Num. of mol.: 1 / Mutation: D30N, C95M, D1030N, C1095A Source method: isolated from a genetically manipulated source Details: CHIMERA PROTEIN WITH LINKER GLY-GLY-SER-SER-GLY (NUMBERED A100 TO A104) THAT COVALENTLY LINK SUB-UNIT A WITH SUB-UNIT B IN THE TETHERED DIMER. Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: group M subtype B (isolate HXB2) / Gene: gag-pol / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin |
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#2: Chemical | ChemComp-ROC / ( |
#3: Water | ChemComp-HOH / |
Sequence details | CHIMERA PROTEIN WITH LINKER GLY-GLY-SER-SER-GLY (NUMBERED A100 TO A104) THAT COVALENTLY LINK SUB- ...CHIMERA PROTEIN WITH LINKER GLY-GLY-SER-SER-GLY (NUMBERED A100 TO A104) THAT COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1-5% SATURATED AMMONIUM SULFATE, 200/100MM PHOSPHATE/CITRATE BUFFER, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→45.426 Å / Num. all: 17298 / Num. obs: 17150 / % possible obs: 99.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.79→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2740 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1LV1 Resolution: 1.795→45.4 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 27.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.795→45.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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