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Yorodumi- PDB-8dch: Crystal Structure of a highly resistant HIV-1 protease Clinical i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dch | |||||||||||||||
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Title | Crystal Structure of a highly resistant HIV-1 protease Clinical isolate PR10x with GRL-0519 (tris-tetrahydrofuran as P2 ligand) | |||||||||||||||
Components | Protease | |||||||||||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / HIV/AIDS / HIV protease / drug resistant clinical mutant / evolution of drug resistance / distal mutations / 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 / molecular replacement / Resolution: 1.25 Å | |||||||||||||||
Authors | Wong-Sam, A.E. / Wang, Y.-F. / Weber, I.T. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Mol.Graph.Model. / Year: 2022 Title: HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics. Authors: Wong-Sam, A. / Wang, Y.F. / Kneller, D.W. / Kovalevsky, A.Y. / 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 | 8dch.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dch.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 8dch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/8dch ftp://data.pdbj.org/pub/pdb/validation_reports/dc/8dch | HTTPS FTP |
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-Related structure data
Related structure data | 8dciC 3nu3S C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 10784.560 Da / Num. of mol.: 2 Mutation: Q7K, L10F, I13V, L19I, K20T, V32I, L33I, E35N, M36I, M46I, G48Q, I54L, L63P, C67E, A71V, T74S, L76V, I84V, L89V, L90M, T91S, I93L, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: Clinical isolate PR76Vmx / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-G52 / ( | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.5 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: Hanging-drop vapor diffusion using equal volumes of protein stock (3.9 mg/mL) and well reservoir solution. Cryoprotected in 30% glycerol. Complex on ice at 1:8 ratio of PR to PI, ...Details: Hanging-drop vapor diffusion using equal volumes of protein stock (3.9 mg/mL) and well reservoir solution. Cryoprotected in 30% glycerol. Complex on ice at 1:8 ratio of PR to PI, crystallized in 1 M NaCl and 0.1 M sodium acetate pH 5.2 |
-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: RAYONIX MX300HE / Detector: CCD / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 67583 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Χ2: 0.999 / Net I/σ(I): 20.7 / Num. measured all: 458139 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 6718 / CC1/2: 0.991 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Χ2: 1.003 / % possible all: 97 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.659
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.25→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.63 Å2 / Biso mean: 20.3406 Å2 / Biso min: 6.68 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.25→50 Å
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Refine LS restraints |
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