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- PDB-2i5j: Crystal structure of HIV-1 reverse transcriptase (RT) in complex ... -
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Basic information
Entry | Database: PDB / ID: 2i5j | |||||||||
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Title | Crystal structure of HIV-1 reverse transcriptase (RT) in complex with DHBNH, an RNASE H inhibitor | |||||||||
![]() | (Reverse transcriptase/ribonuclease H ...) x 2 | |||||||||
![]() | TRANSFERASE / AIDS / HIV / REVERSE TRANSCRIPTASE / RT / RNase H Inhibitor / RNHI / STRUCTURE-BASED DRUG DESIGN / PROTEIN-INHIBITOR COMPLEX / DRUG RESISTANCE | |||||||||
Function / homology | ![]() HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / 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 / proteolysis / DNA binding / zinc ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Himmel, D.M. / Sarafianos, S.G. / Knight, J.L. / Levy, R.M. / Arnold, E. | |||||||||
![]() | ![]() Title: HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. Authors: Himmel, D.M. / Sarafianos, S.G. / Dharmasena, S. / Hossain, M.M. / McCoy-Simandle, K. / Ilina, T. / Clark, A.D. / Knight, J.L. / Julias, J.G. / Clark, P.K. / Krogh-Jespersen, K. / Levy, R.M. ...Authors: Himmel, D.M. / Sarafianos, S.G. / Dharmasena, S. / Hossain, M.M. / McCoy-Simandle, K. / Ilina, T. / Clark, A.D. / Knight, J.L. / Julias, J.G. / Clark, P.K. / Krogh-Jespersen, K. / Levy, R.M. / Hughes, S.H. / Parniak, M.A. / Arnold, E. #1: ![]() Title: Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-nucleoside Inhibitors Effective Against a Broad Range of Drug-Resistant Strains Authors: Himmel, D.M. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Benjahad, A. / Oumouch, S. / Guillemont, J. / Coupa, S. / Poncelet, A. / Csoka, I. / Meyer, C. / Andries, K. / Nguyen, C.H. / Grierson, D.S. / Arnold, E. #2: ![]() Title: Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA Authors: Sarafianos, S.G. / Das, K. / Tantillo, C. / Clark Jr., A.D. / Ding, J. / Whitcomb, J.M. / Boyer, P.L. / Hughes, S.H. / Arnold, E. #3: ![]() Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent ...Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent and Effective Against Wild-Type and Drug-Resistant HIV-1 Variants Authors: Das, K. / Clark Jr., A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M.H. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. ...Authors: Das, K. / Clark Jr., A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M.H. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, H. / Lichtenstein, M.A. / Andries, K. / Pauwels, R. / De Bethune, M.-P. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A.J. / Arnold, E. #4: ![]() Title: Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution. Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E. #5: ![]() Title: Structure of unliganded HIV-1 reverse transcriptase t 2.7 A resolution: implications of conformational hanges for polymerization and inhibition mechanisms Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Arnold, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.5 KB | Display | ![]() |
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PDB format | ![]() | 170.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 48.2 KB | Display | |
Data in CIF | ![]() | 64.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2be2S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Reverse transcriptase/ribonuclease H ... , 2 types, 2 molecules AB
#1: Protein | Mass: 63659.906 Da / Num. of mol.: 1 / Fragment: residues 599-1150 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 50152.648 Da / Num. of mol.: 1 / Fragment: residues 599-1027 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P03366, UniProt: Q8UM83*PLUS, RNA-directed DNA polymerase |
-Sugars , 2 types, 5 molecules ![](data/chem/img/GLC.gif)
#3: Polysaccharide | #4: Sugar | |
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-Non-polymers , 3 types, 38 molecules ![](data/chem/img/K05.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-K05 / ( |
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#6: Chemical | ChemComp-MG / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 50 mM Imidazole pH 6.4, 100 mM Ammonium Sulfate, 15 mM Magnesium Sulfate, 0.6 mM DHBNH, 4% Glucose, 10.5% PEG 8000, 2 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→26 Å / Num. all: 27482 / Num. obs: 24789 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 5.2 % / Biso Wilson estimate: 66.849 Å2 / Rsym value: 0.101 / Χ2: 1.001 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3.15→3.26 Å / Redundancy: 2.8 % / Num. unique all: 2011 / Rsym value: 0.805 / Χ2: 0.847 / % possible all: 74.4 |
-Phasing
Phasing MR | Rfactor: 0.365 / R rigid body: 0.351 / Cor.coef. Fo:Fc: 0.759 / Cor.coef. Io to Ic: 0.683
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Phasing dm shell | Resolution: 3→25 Å / Delta phi final: 0.123 / FOM : 0.125 / Reflection: 25136 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BE2 Resolution: 3.15→25.71 Å / Rfactor Rfree error: 0.01 / FOM work R set: 0.819 / Data cutoff high absF: 197616.641 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.394 Å2 / ksol: 0.277 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.15→25.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.35 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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