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- PDB-4i2p: Crystal structure of HIV-1 reverse transcriptase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4i2p | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase in complex with rilpivirine (TMC278) based analogue | ||||||
![]() | (Gag-Pol polyprotein) x 2 | ||||||
![]() | HYDROLASE / TRANSFERASE/INHIBITOR / P51/P66 / hetero dimer / NNRTI / nonnucleoside inhibitor / AIDS / HIV / DNA recombination / RNA-directed DNA polymerase / DNA polymerase / endonuclease / multifunctional enzyme / transferase / TRANSFERASE-INHIBITOR complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Patel, D. / Bauman, J.D. / Das, K. / Arnold, E. | ||||||
![]() | ![]() Title: A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants. Authors: Johnson, B.C. / Pauly, G.T. / Rai, G. / Patel, D. / Bauman, J.D. / Baker, H.L. / Das, K. / Schneider, J.P. / Maloney, D.J. / Arnold, E. / Thomas, C.J. / Hughes, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.9 KB | Display | ![]() |
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PDB format | ![]() | 170.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 714.9 KB | Display | ![]() |
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Full document | ![]() | 731.4 KB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 53.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: p66 (UNP Residues 600-1154) / Mutation: C879S, K771A, K772A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Production host: ![]() ![]() References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
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#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: p51 (UNP Residues 600-1077) / Mutation: C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Production host: ![]() ![]() References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
#3: Chemical | ChemComp-G73 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 50 mM imidazole pH 6.6, 100 mM ammonium sulfate, 15 mM manganese sulfate, 10 mM spermine, 5 mM TCEP, 11% (w/w) PEG 8000, and 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.296→107.73 Å / Num. obs: 55926 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.058 Å2 / ksol: 0.39 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2964→41.294 Å
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Refine LS restraints |
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LS refinement shell |
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