+Open data
-Basic information
Entry | Database: PDB / ID: 4be2 | ||||||
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Title | PFV intasome with inhibitor XZ-259 | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / RECOMBINATION / INHIBITOR / RECOMBINATION-INHIBITOR-DNA COMPLEX | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / 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 ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / 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 / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | HUMAN SPUMARETROVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.38 Å | ||||||
Authors | Hare, S. / Cherepanov, P. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase. Authors: Metifiot, M. / Maddali, K. / Johnson, B.C. / Hare, S. / Smith, S.J. / Zhao, X.Z. / Marchand, C. / Burke, T.R. / Hughes, S.H. / Cherepanov, P. / Pommier, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4be2.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4be2.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 4be2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4be2 ftp://data.pdbj.org/pub/pdb/validation_reports/be/4be2 | HTTPS FTP |
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-Related structure data
Related structure data | 4bdyC 4bdzC 4be0C 4be1C 3l2t C: citing same article (ref.) S: Starting model for refinement |
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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: 44456.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN SPUMARETROVIRUS / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P14350, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN SPUMARETROVIRUS |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN SPUMARETROVIRUS |
-Non-polymers , 6 types, 333 molecules
#4: Chemical | ChemComp-ZN / | ||||||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | ChemComp-XZ2 / | #9: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | XZ-259 (XZ2): SEE ATTACHED TIFF IMAGE |
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Sequence details | N-TERMINAL 'GLY-PRO-GLY' IS A RESULT OF CLONING AND PROTEOLYSIS OF HIS-TAG RESIDUES 217-218 (GLY- ...N-TERMINAL 'GLY-PRO-GLY' IS A RESULT OF CLONING AND PROTEOLYSI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.11 Å3/Da / Density % sol: 75.75 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.35 M AMMONIUM SULFATE, 25% (V/V) GLYCEROL, 4.8% (V/V) 1,6-HEXANEDIOL, 50 MM MES-NAOH, 1MM EDTA, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0389 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0389 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→40 Å / Num. obs: 60396 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.38→2.51 Å / Redundancy: 8 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3L2T 3l2t Resolution: 2.38→38.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.787 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 55.895 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→38.72 Å
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