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Yorodumi- PDB-3ka2: Crystal structure of chemically synthesized 203 amino acid 'coval... -
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-Basic information
Entry | Database: PDB / ID: 3ka2 | ||||||
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Title | Crystal structure of chemically synthesized 203 amino acid 'covalent dimer' [L-Ala;Gly51']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor at 1.4 A resolution | ||||||
Components | [L-Ala51;Gly51']HIV-1 protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / beta-barrel / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molrep v.5 / Resolution: 1.4 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 | 3ka2.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ka2.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ka2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ka2_validation.pdf.gz | 948.7 KB | Display | wwPDB validaton report |
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Full document | 3ka2_full_validation.pdf.gz | 956.1 KB | Display | |
Data in XML | 3ka2_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3ka2_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/3ka2 ftp://data.pdbj.org/pub/pdb/validation_reports/ka/3ka2 | HTTPS FTP |
-Related structure data
Related structure data | 3fsmC 3hauSC 3hawC 3hboC 3hdkC 3hloC 3iawC 3nwqC 3nwxC 3nxeC 3nxnC 3nygC 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
#1: Protein | [ Mass: 21905.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P03369*PLUS, HIV-1 retropepsin |
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#2: Chemical | ChemComp-2NC / |
#3: 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: 2.11 Å3/Da / Density % sol: 41.71 % |
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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% (V/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: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2007 Details: BENT CONICAL SI-MIRROR (RH COATING); BENT GE(111) MONOCHROMATOR |
Radiation | Monochromator: BENT GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 36259 / % possible obs: 98.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.46 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.85 / Num. unique all: 3370 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: Molrep v.5 Starting model: 3HAU Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.619 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.072 / 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: 25.362 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.403→1.439 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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