+Open data
-Basic information
Entry | Database: PDB / ID: 4bdy | ||||||
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Title | PFV intasome with inhibitor XZ-89 | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / PROTEIN-DNA COMPLEX / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / DNA-BINDING / ZINC BINDING / HHCC MOTIF / RECOMBINATION / INHIBITOR / RECOMBINATION-INHIBITOR-DNA COMPLEX | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / aspartic-type endopeptidase activity / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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: 2.52 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 | 4bdy.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bdy.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bdy_validation.pdf.gz | 816.2 KB | Display | wwPDB validaton report |
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Full document | 4bdy_full_validation.pdf.gz | 823.8 KB | Display | |
Data in XML | 4bdy_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 4bdy_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/4bdy ftp://data.pdbj.org/pub/pdb/validation_reports/bd/4bdy | HTTPS FTP |
-Related structure data
Related structure data | 4bdzC 4be0C 4be1C 4be2C 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, 301 molecules
#4: Chemical | ChemComp-ZN / | ||||||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | ChemComp-CIJ / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.8 % |
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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: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→40 Å / Num. obs: 51082 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.52→2.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3L2T 3l2t Resolution: 2.52→39.12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.04 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.183 / 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: 56.244 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→39.12 Å
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