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Yorodumi- PDB-7taz: Crystal structure of HIV-1 reverse transcriptase (RT) in complex ... -
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-Basic information
Entry | Database: PDB / ID: 7taz | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase (RT) in complex with VM-1500A, a non-nucleoside RT inhibitor | ||||||
Components |
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Keywords | TRANSFERASE/INHIBITOR / Reverse Transcriptase / HIV-1 / Polymerase / NNRTI / VM-1500 / Elsulfavirine / VIRAL PROTEIN / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Snyder, A.A. / Risener, C.J. / Kirby, K.A. / Sarafianos, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of HIV-1 reverse transcriptase (RT) in complex with VM-1500A, a non-nucleoside RT inhibitor Authors: Snyder, A.A. / Risener, C.J. / Kirby, K.A. / Stefan, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7taz.cif.gz | 411.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7taz.ent.gz | 335.2 KB | Display | PDB format |
PDBx/mmJSON format | 7taz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/7taz ftp://data.pdbj.org/pub/pdb/validation_reports/ta/7taz | HTTPS FTP |
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-Related structure data
Related structure data | 4g1qS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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 / Mutation: K172A, K173A, C180S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET52a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
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#2: Protein | Mass: 50096.539 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET52a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-VM5 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8,000, ammonium sulfate, Bis tris propane, ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→48.62 Å / Num. obs: 49968 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 19.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G1Q Resolution: 2.4→48.62 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2567 / WRfactor Rwork: 0.2389 / FOM work R set: 0.8245 / SU B: 16.971 / SU ML: 0.186 / SU R Cruickshank DPI: 0.4154 / SU Rfree: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 351.53 Å2 / Biso mean: 88.277 Å2 / Biso min: 36.5 Å2
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Refinement step | Cycle: final / Resolution: 2.4→48.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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