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Yorodumi- PDB-4y1d: Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y1d | ||||||
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Title | Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE BINDING PROTEIN / DNA INTEGRATION / AIDS / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING / VIRAL PROTEIN / RNASEH / LEDGF / LENS EPITHELIUM DERIVED GROWTH FACTOR / VIRAL PROTEIN-PEPTIDE COMPLEX / TRANSFERASE-TRANSFERASE BINDING PROTEIN 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 / endonuclease activity / 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 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Wielens, J. / Chalmers, D.K. | ||||||
Citation | Journal: To Be Published Title: HEXAPEPTIDE MIMETICS OF LEDGF IN COMPLEX WITH HIV-1 INTEGRASE Authors: Northfield, S.E. / Wielens, J. / Headey, S.J. / Mulcair, M. / Scanlon, M.J. / Parker, M.W. / Thompson, P.E. / Chalmers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y1d.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y1d.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 4y1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/4y1d ftp://data.pdbj.org/pub/pdb/validation_reports/y1/4y1d | HTTPS FTP |
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-Related structure data
Related structure data | 4y1cC 3wneS 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 / Protein/peptide , 2 types, 3 molecules ABD
#1: Protein | Mass: 18215.648 Da / Num. of mol.: 2 / Fragment: residues 50-212 / Mutation: C56S, W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: PET23B / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / References: UniProt: F2WR39, UniProt: P12497*PLUS #2: Protein/peptide | | Mass: 725.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 116 molecules
#3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.8M AMMONIUM SULFATE, 0.15M SODIUM CITRATE, 5MM CADMIUM CHLORIDE, PH 4.6 PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 23862 / % possible obs: 94.3 % / Redundancy: 6.72 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.07 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 4.5 % / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WNE Resolution: 1.93→19.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.595 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 38.39 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→19.5 Å
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