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Yorodumi- PDB-7maq: Drug Resistant HIV-1 Protease (L10F, V32I, L33F, K45I, A71V, V82I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7maq | ||||||
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Title | Drug Resistant HIV-1 Protease (L10F, V32I, L33F, K45I, A71V, V82I, I84V) in Complex with DRV | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / drug resistance / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information RNA stem-loop binding / host cell / 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 ...RNA stem-loop binding / host cell / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Lockbaum, G.J. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Drug Resistant HIV-1 Protease (L10F, V32I, L33F, K45I, A71V, V82I, I84V) in Complex with DRV Authors: Lockbaum, G.J. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7maq.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7maq.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 7maq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/7maq ftp://data.pdbj.org/pub/pdb/validation_reports/ma/7maq | HTTPS FTP |
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-Related structure data
Related structure data | 6dgxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 99 / Label seq-ID: 1 - 99
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-Components
#1: Protein | Mass: 10925.924 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: L10F, V32I, L33F, K45I, A71V, V82I, I84V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Strain: isolate BRU/LAI / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-017 / ( | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 23-24% (w/v) Ammonium Sulfate, 0.1 M Bis-Tris-Methane-HCl Buffer pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.5 |
Reflection | Resolution: 1.93→24.9 Å / Num. obs: 13684 / % possible obs: 99.5 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 46 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1314 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6dgx Resolution: 1.93→24.872 Å / Cross valid method: THROUGHOUT / σ(F): 6.2 / Phase error: 27.74 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.97 Å2 / Biso mean: 38.0262 Å2 / Biso min: 15.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.93→24.872 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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