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- PDB-2ic3: Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcripta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ic3 | ||||||
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Title | Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with Nonnucleoside Inhibitor HBY 097 | ||||||
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![]() | TRANSFERASE / RT / NNRTI / NONNUCLEOSIDE INHIBITOR / DRUG RESISTANCE / HIV / AIDS / DRUG DESIGN | ||||||
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 / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Das, K. / Arnold, E. | ||||||
![]() | ![]() Title: Crystal Structures of Clinically Relevant Lys103Asn/Tyr181Cys Double Mutant HIV-1 Reverse Transcriptase in Complexes with ATP and Non-nucleoside Inhibitor HBY 097. Authors: Das, K. / Sarafianos, S.G. / Clark, A.D. / Boyer, P.L. / Hughes, S.H. / Arnold, E. #1: ![]() Title: Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms Authors: Hsiou, Y. / Ding, J. / Das, K. / D Clark, A. / Hughes, S.H. / Arnold, E. #2: ![]() Title: Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark, A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith, R.H. / Kroeger Smith, M.B. / ...Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark, A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith, R.H. / Kroeger Smith, M.B. / Michejda, C.J. / Hughes, S.H. / Arnold, E. #3: ![]() Title: Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance. Authors: Hsiou, Y. / Das, K. / Ding, J. / Clark, A.D. / Kleim, J.P. / Winkler, I. / Riess, G. / Hughes, S.H. / Arnold, E. #4: ![]() Title: The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance. Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark, A.D. / Boyer, P.L. / Lewi, P. / Janssen, P.A. / Kleim, J.P. / Hughes, S.H. / Arnold, E. #5: ![]() 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, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, ...Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / 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. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A. / 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 | ![]() | 212 KB | Display | ![]() |
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PDB format | ![]() | 167.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 803.5 KB | Display | ![]() |
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Full document | ![]() | 889.1 KB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 64.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iajC ![]() 1s6qS C: citing same article ( 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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Unit cell |
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Details | HETERODIMER of p66 and p51 subunits |
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Components
#1: Protein | Mass: 64425.855 Da / Num. of mol.: 1 / Fragment: p66 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: BH10 ISOLATE / Gene: pol / Production host: ![]() ![]() |
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#2: Protein | Mass: 51970.562 Da / Num. of mol.: 1 / Fragment: p51 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: BH10 ISOLATE / Gene: pol / Production host: ![]() ![]() |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-HBY / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 8000, BIS_TRIS PROPANE, AMMONIUM SULFATE, GLYCEROL, MNCL2, HBY 097, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→40 Å / Num. obs: 26685 / % possible obs: 90.1 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Χ2: 1.184 / Net I/σ(I): 24.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S6Q Resolution: 3→19.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 645411.812 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.852 Å2 / ksol: 0.232 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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