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Yorodumi- PDB-3qrm: HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-arm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qrm | ||||||
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Title | HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Aspartyl Protease / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / 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 | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.731 Å | ||||||
Authors | Lindemann, I. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Design of a series of novel three-armed pyrrolidine-based inhibitors for HIV-1 protease Authors: Lindemann, I. / Klee, N. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qrm.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qrm.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qrm_validation.pdf.gz | 777.9 KB | Display | wwPDB validaton report |
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Full document | 3qrm_full_validation.pdf.gz | 779.1 KB | Display | |
Data in XML | 3qrm_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3qrm_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/3qrm ftp://data.pdbj.org/pub/pdb/validation_reports/qr/3qrm | HTTPS FTP |
-Related structure data
Related structure data | 3qbfC 3qpjC 3qroC 3qrsC 2pqzS 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
#1: Protein | Mass: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K L33I L63I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE) Plasmid: pET24a / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-NK7 / | #3: Chemical | #4: Chemical | ChemComp-DTD / | #5: Water | ChemComp-HOH / | Nonpolymer details | NEXT TO THE DTD MOLECULE IN THE BINDING POCKET WE OBSERVED ADDITIONAL DENSITY (5.00 SIGMA LEVEL) ...NEXT TO THE DTD MOLECULE IN THE BINDING POCKET WE OBSERVED ADDITIONAL | |
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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: 2.68 Å3/Da / Density % sol: 54.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 700mM NaCl, 100mM Na citrate, 100mM DTT, 3mM NaN3, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2010 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. all: 24130 / Num. obs: 24130 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.59 Å2 / Rsym value: 0.044 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 6 / Num. unique all: 1150 / Rsym value: 0.19 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQZ Resolution: 1.731→25.701 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.2 / σ(F): 0 / Phase error: 18.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.573 Å2 / ksol: 0.374 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.18 Å2 / Biso mean: 16.0412 Å2 / Biso min: 3.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.731→25.701 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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