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Yorodumi- PDB-3nyg: X-ray structure of ester chemical analogue [O-Gly51,O-Gly51']HIV-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nyg | ||||||||||||
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Title | X-ray structure of ester chemical analogue [O-Gly51,O-Gly51']HIV-1 protease complexed with MVT-101 inhibitor | ||||||||||||
Components | protease | ||||||||||||
Keywords | hydrolase/hydrolase inhibitor / beta-barrel / hydrolase-hydrolase 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 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||||||||
Authors | Torbeev, V.Y. / Kent, S.B.H. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Authors: Torbeev, V.Y. / Raghuraman, H. / Hamelberg, D. / Tonelli, M. / Westler, W.M. / Perozo, E. / Kent, S.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nyg.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nyg.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/3nyg ftp://data.pdbj.org/pub/pdb/validation_reports/ny/3nyg | HTTPS FTP |
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-Related structure data
Related structure data | 3fsmC 3hauC 3hawC 3hboC 3hdkC 3hloC 3iawC 3ka2C 3nwqC 3nwxC 3nxeC 3nxnC 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
#1: Protein | Mass: 10761.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical protein synthesis / References: UniProt: P03369*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-2NC / | #3: Chemical | #4: 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: 2.12 Å3/Da / Density % sol: 42.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Citrate, 0.2 M Sodium Phosphate, 30% (w/v) Ammonium Sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2007 Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 33147 / % possible obs: 99.5 % / Observed criterion σ(F): 24.9 / Observed criterion σ(I): 24.9 / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.4 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.407 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.075 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.569 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.446→1.483 Å / 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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