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- PDB-5j2p: HIV-1 reverse transcriptase in complex with DNA that has incorpor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j2p | ||||||||||||||||||||||||
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Title | HIV-1 reverse transcriptase in complex with DNA that has incorporated EFdA-MP at the P-(post-translocation) site and a second EFdA-MP at the N-(pre-translocation) site | ||||||||||||||||||||||||
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![]() | transferase/dna / HIV-1 / reverse transcriptase / RT / DNA / double stranded DNA / dsDNA / EFdA / 4'-ethynyl-2-fluoro-2'-deoxyadenosine / EFdA-monophosphate / EFdA-MP / inhibitors / NRTI / TDRTI / translocation defective / P site / N site / pre-translocation / post-translocation / transferase-dna complex | ||||||||||||||||||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Salie, Z.L. / Kirby, K.A. / Sarafianos, S.G. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA). Authors: Salie, Z.L. / Kirby, K.A. / Michailidis, E. / Marchand, B. / Singh, K. / Rohan, L.C. / Kodama, E.N. / Mitsuya, H. / Parniak, M.A. / Sarafianos, S.G. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 474 KB | Display | ![]() |
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PDB format | ![]() | 381.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014.5 KB | Display | ![]() |
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Full document | ![]() | 1020.9 KB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j2mSC ![]() 5j2nC ![]() 5j2qC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Reverse transcriptase, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 64521.895 Da / Num. of mol.: 1 / Mutation: Q258C, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate HXB2 / Gene: gag-pol / Plasmid: pCDFDuet1 / Production host: ![]() ![]() References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein | Mass: 51382.984 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate HXB2 / Gene: gag-pol / Plasmid: pRSFDuet1 / Production host: ![]() ![]() References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 6871.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#4: DNA chain | Mass: 8398.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 423 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/6FM.gif)
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#5: Chemical | ChemComp-MG / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8% PEG4000, 25mM MES pH 6.0, 5mM magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 2, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.53→63.78 Å / Num. obs: 46900 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.041 / Rrim(I) all: 0.111 / Net I/σ(I): 16.7 / Num. measured all: 337771 / Scaling rejects: 7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.7 % / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 5J2M Resolution: 2.53→63.78 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.66 Å2 / Biso mean: 51.6027 Å2 / Biso min: 27.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.53→63.78 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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