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Yorodumi- PDB-4obf: Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Proteas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4obf | ||||||
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Title | Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease Variant (D30N/N88D) in Complex with the p1-p6 substrate variant (S451N) | ||||||
Components |
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Keywords | HYDROLASE / Co-evolution / Resistance | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / 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 budding via host ESCRT complex / 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 / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å | ||||||
Authors | Kolli, M. | ||||||
Citation | Journal: J.Virol. / Year: 2014 Title: HIV-1 protease-substrate coevolution in nelfinavir resistance. Authors: Kolli, M. / Ozen, A. / Kurt-Yilmaz, N. / 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 | 4obf.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4obf.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 4obf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4obf ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obf | HTTPS FTP |
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-Related structure data
Related structure data | 4obdC 4obgC 4obhC 4objC 4obkC 1t3rS 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 10814.804 Da / Num. of mol.: 4 / Mutation: Q7K, D25N, D30N, V64I, N88D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: group M subtype B (isolate ARV2/SF2) / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin #2: Protein/peptide | Mass: 1200.350 Da / Num. of mol.: 2 / Fragment: UNP residues 446-455 / Mutation: S8N / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03349 |
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-Non-polymers , 5 types, 204 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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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: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 32% Ammonium Sulphate, 63mM Sodium Citrate, 126mM Sodium Phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2009 / Details: Mirrors |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 41265 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.066 / Net I/σ(I): 21.12 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.713 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 47.12 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1T3R Resolution: 1.68→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.485 / SU ML: 0.088 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.068 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→30 Å
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Refine LS restraints |
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