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Yorodumi- PDB-1mtr: HIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mtr | ||||||
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Title | HIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC INHIBITOR | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ASPARTYL PROTEINASE / AIDS / 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 / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / 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 1 | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.75 Å | ||||||
Authors | Wickramasinghe, W. / Begun, J. / Martin, J.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1996 Title: Substrate-based cyclic peptidomimetics of Phe-Ile-Val that inhibit HIV-1 protease using a novel enzyme-binding mode. Authors: March, D.R. / Abbenante, G. / Bergman, D.A. / Brinkworth, R.I. / Wickramasinghe, W. / Begun, J. / Martin, J.L. / Fairlie, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mtr.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mtr.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mtr_validation.pdf.gz | 494.8 KB | Display | wwPDB validaton report |
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Full document | 1mtr_full_validation.pdf.gz | 497.2 KB | Display | |
Data in XML | 1mtr_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1mtr_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/1mtr ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mtr | HTTPS FTP |
-Related structure data
Related structure data | 1cpiS 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: 10765.687 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-PI6 / [ | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 596.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H48N4O6 References: tert-butyl [(1S,2S)-1-benzyl-2-hydroxy-3-{[(8S,11R)-8-[(1R)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]amino}propyl]carbamate #4: Water | ChemComp-HOH / | Sequence details | GLN 7 WAS REPLACED BY LYS TO PREVENT AUTOCLEAVAGE. LEU 33 WAS REPLACED BY ILE TO PREVENT ...GLN 7 WAS REPLACED BY LYS TO PREVENT AUTOCLEAVA | |
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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: 2.11 Å3/Da / Density % sol: 44 % | ||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.4 / Method: vapor diffusion | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 28, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 16528 / % possible obs: 85.9 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.75→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.42 / % possible all: 69.2 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1CPI Resolution: 1.75→8 Å / σ(F): 2 Details: RESIDUES 50 AND 51 IN THE FLAP REGION OF BOTH SUBUNITS ARE DISORDERED AND WERE MODELLED IN TWO CONFORMATIONS. HOWEVER, THESE REGIONS OF THE STRUCTURE HAVE RELATIVELY POOR GEOMETRY.
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Displacement parameters | Biso mean: 18.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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