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Yorodumi- PDB-1ikv: K103N Mutant HIV-1 Reverse Transcriptase in Complex with Efivarenz -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ikv | ||||||
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Title | K103N Mutant HIV-1 Reverse Transcriptase in Complex with Efivarenz | ||||||
Components | (POL POLYPROTEIN) x 2 | ||||||
Keywords | TRANSFERASE / Heterodimer / protein-inhibitor complex | ||||||
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: 3 Å | ||||||
Authors | Lindberg, J. / Unge, T. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2002 Title: Structural basis for the inhibitory efficacy of efavirenz (DMP-266), MSC194 and PNU142721 towards the HIV-1 RT K103N mutant. Authors: Lindberg, J. / Sigurdsson, S. / Lowgren, S. / Andersson, H.O. / Sahlberg, C. / Noreen, R. / Fridborg, K. / Zhang, H. / Unge, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ikv.cif.gz | 207.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ikv.ent.gz | 163.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ikv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ikv_validation.pdf.gz | 746.1 KB | Display | wwPDB validaton report |
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Full document | 1ikv_full_validation.pdf.gz | 791.5 KB | Display | |
Data in XML | 1ikv_validation.xml.gz | 40 KB | Display | |
Data in CIF | 1ikv_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/1ikv ftp://data.pdbj.org/pub/pdb/validation_reports/ik/1ikv | HTTPS FTP |
-Related 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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Details | The biological assembly is a heterodimer |
-Components
#1: Protein | Mass: 64500.965 Da / Num. of mol.: 1 / Mutation: K103N, E478Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: BH10 / Plasmid: PETd / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 49912.344 Da / Num. of mol.: 1 / Mutation: K103N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: BH10 / Plasmid: PETd / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-EFZ / (-)- |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.63 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 270 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0232 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 2000 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0232 Å / Relative weight: 1 |
Reflection | Resolution: 3→24.84 Å / Num. all: 29822 / Num. obs: 29152 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 3→24.84 Å / Redundancy: 2 % / Rmerge(I) obs: 0.63 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 48782 |
Reflection shell | *PLUS Lowest resolution: 3.11 Å / % possible obs: 97.8 % / Num. unique obs: 2856 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2624691.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.43 Å2 / ksol: 0.251 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.229 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.401 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.348 |