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Yorodumi- PDB-3vqe: HIV-1 IN core domain in complex with [1-(4-fluorophenyl)-5-methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vqe | ||||||
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Title | HIV-1 IN core domain in complex with [1-(4-fluorophenyl)-5-methyl-1H-pyrazol-4-yl]methanol | ||||||
Components | POL polyprotein | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / RNAseH / DNA binding / DNA cleavage / DNA integration / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / aspartic-type endopeptidase activity / DNA recombination / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / aspartic-type endopeptidase activity / DNA recombination / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wielens, J. / Chalmers, D.K. / Parker, M.W. / Scanlon, M.J. | ||||||
Citation | Journal: J Biomol Screen / Year: 2013 Title: Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? Authors: Wielens, J. / Headey, S.J. / Rhodes, D.I. / Mulder, R.J. / Dolezal, O. / Deadman, J.J. / Newman, J. / Chalmers, D.K. / Parker, M.W. / Peat, T.S. / Scanlon, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vqe.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vqe.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vqe_validation.pdf.gz | 461.9 KB | Display | wwPDB validaton report |
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Full document | 3vqe_full_validation.pdf.gz | 465.4 KB | Display | |
Data in XML | 3vqe_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3vqe_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/3vqe ftp://data.pdbj.org/pub/pdb/validation_reports/vq/3vqe | HTTPS FTP |
-Related structure data
Related structure data | 3vq4C 3vq5C 3vq6C 3vq7C 3vq8C 3vq9C 3vqaC 3vqbC 3vqcC 3vqdC 3vqpC 3vqqC 4ah9C 4ahrC 4ahsC 4ahtC 4ahuC 4ahvC 3l3uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17101.393 Da / Num. of mol.: 2 / Fragment: integrase core domain, UNP residues 771-927 / Mutation: C56S, S123G, T124A, K127R, W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL43 / Gene: pol / Plasmid: PeT23b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72498 |
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-Non-polymers , 5 types, 89 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.6M AmSO4, 0.1M Na Citrate pH 4.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9567 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 22, 2008 / Details: mirrors |
Radiation | Monochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9567 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 31059 / Num. obs: 30896 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 21.95 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.033 / Net I/σ(I): 31.68 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.15 / Rsym value: 0.308 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3l3u Resolution: 1.7→26.826 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.14 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→26.826 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: 11
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