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Yorodumi- PDB-3lan: Crystal structure of HIV-1 reverse transcriptase in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3lan | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase in complex with N1-butyl pyrimidinedione non-nucleoside inhibitor | ||||||
Components | HIV Reverse transcriptase | ||||||
Keywords | TRANSFERASE / HIV / reverse transcriptase / RT / NNRTI | ||||||
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 / Assembly Of The HIV Virion / HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Lansdon, E.B. / Mitchell, M.L. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: N1-Alkyl pyrimidinediones as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Authors: Mitchell, M.L. / Son, J.C. / Guo, H. / Im, Y.A. / Cho, E.J. / Wang, J. / Hayes, J. / Wang, M. / Paul, A. / Lansdon, E.B. / Chen, J.M. / Graupe, D. / Rhodes, G. / He, G.X. / Geleziunas, R. / Xu, L. / Kim, C.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lan.cif.gz | 207 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lan.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lan_validation.pdf.gz | 776 KB | Display | wwPDB validaton report |
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Full document | 3lan_full_validation.pdf.gz | 807.4 KB | Display | |
Data in XML | 3lan_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 3lan_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/3lan ftp://data.pdbj.org/pub/pdb/validation_reports/la/3lan | HTTPS FTP |
-Related structure data
Related structure data | 3lalC 3lamC 1vrtS 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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Unit cell |
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-Components
#1: Protein | Mass: 64562.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, RNA-directed DNA polymerase #2: Chemical | ChemComp-KBT / | #3: Chemical | ChemComp-SO4 / #4: 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: 2.72 Å3/Da / Density % sol: 54.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.3M ammonium sulfate, 100mM cacodylate, 5mM sodium malonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2007 |
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 43129 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.55→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.5 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1VRT Resolution: 2.55→29.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 153326.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.3903 Å2 / ksol: 0.313419 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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