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- PDB-1mtr: HIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mtr | ||||||
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Title | HIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC INHIBITOR | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ASPARTYL PROTEINASE / AIDS / ASPARTYL PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Wickramasinghe, W. / Begun, J. / Martin, J.L. | ||||||
![]() | 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.1 KB | Display | ![]() |
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PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494.8 KB | Display | ![]() |
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Full document | ![]() | 497.2 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cpiS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PI6 / [ | ![]() 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: ![]() |
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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 |
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Processing
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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