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Yorodumi- PDB-1dtt: CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH ... -
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Entry | Database: PDB / ID: 1dtt | ||||||
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Title | CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH PETT-2 (PETT130A94) | ||||||
Components |
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Keywords | HYDROLASE/TRANSFERASE / HIV-1 reverse transcriptase AIDS / non-nucleoside inhibitor / drug design / HYDROLASE-TRANSFERASE COMPLEX | ||||||
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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / 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 / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Ren, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Phenylethylthiazolylthiourea (PETT) non-nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases. Structural and biochemical analyses. Authors: Ren, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K. #1: Journal: J.Med.Chem. / Year: 1999 Title: Crystallographic analysis of the binding modes of thiazoloisoindolinone non-nucleoside inhibitors to HIV-1 reverse transcriptase and comparison with modeling studies. Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Stuart, D.I. / Stammers, D.K. #2: Journal: J.Med.Chem. / Year: 1999 Title: Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants. Authors: Hopkins, A.L. / Ren, J. / Tanaka, H. / Baba, M. / Okamato, M. / Stuart, D.I. / Stammers, D.K. #3: Journal: Biochemistry / Year: 1998 Title: Crystal structures of HIV-1 reverse transcriptase in complex with carboxanilide derivatives. Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Warren, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: 3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes. Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Jones, E.Y. / Kirby, I. / Keeling, J. / Ross, C.K. / Larder, B.A. / Stuart, D.I. / Stammers, D.K. #5: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration. Authors: Esnouf, R.M. / Ren, J. / Garman, E.F. / Somers, D.O. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I. #6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this nonnucleoside inhibitor. Authors: Esnouf, R.M. / Ren, J. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I. #7: Journal: J.Med.Chem. / Year: 1996 Title: Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors. Authors: Hopkins, A.L. / Ren, J. / Esnouf, R.M. / Willcox, B.E. / Jones, E.Y. / Ross, C. / Miyasaka, T. / Walker, R.T. / Tanaka, H. / Stammers, D.K. / Stuart, D.I. #8: Journal: Structure / Year: 1995 Title: The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design. Authors: Ren, J. / Esnouf, R. / Hopkins, A. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D. #9: Journal: Nat.Struct.Biol. / Year: 1995 Title: High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Authors: Ren, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D. #10: Journal: Nat.Struct.Biol. / Year: 1995 Title: Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors. Authors: Esnouf, R. / Ren, J. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D. #11: Journal: J.Mol.Biol. / Year: 1994 Title: Crystals of HIV-1 reverse transcriptase diffracting to 2.2 A resolution. Authors: Stammers, D.K. / Somers, D.O. / Ross, C.K. / Kirby, I. / Ray, P.H. / Wilson, J.E. / Norman, M. / Ren, J.S. / Esnouf, R.M. / Garman, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dtt.cif.gz | 201.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dtt.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dtt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dtt_validation.pdf.gz | 827.7 KB | Display | wwPDB validaton report |
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Full document | 1dtt_full_validation.pdf.gz | 880 KB | Display | |
Data in XML | 1dtt_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 1dtt_validation.cif.gz | 55.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtt ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtt | HTTPS FTP |
-Related 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: 64594.949 Da / Num. of mol.: 1 / Fragment: P66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Bacteria (eubacteria) / References: UniProt: P04585 |
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#2: Protein | Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: P51 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Bacteria (eubacteria) / References: UniProt: P04585 |
#3: Chemical | ChemComp-FTC / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: see reference 11, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Details: Stammers, D.K., (1994) J.Mol.Biol., 242, 586. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 3→30 Å / Num. obs: 21409 / % possible obs: 89.2 % / Observed criterion σ(I): -1.5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.4 | |||||||||||||||
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.592 / Num. unique all: 1793 / % possible all: 76.7 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 86903 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 81.7 % / Num. unique obs: 1771 |
-Processing
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Refinement | Resolution: 3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Due to the low ratio between the number of reflections and the number of parameters to be refined, positional restraints were applied to all atoms distant from the NNRTI-binding site ...Details: Due to the low ratio between the number of reflections and the number of parameters to be refined, positional restraints were applied to all atoms distant from the NNRTI-binding site (defined as greater than 25 anstrom from the CA atom of residue 188) throughout the refinement.
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.199 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |