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Yorodumi- PDB-1b6m: HIV-1 PROTEASE COMPLEXED WITH MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b6m | ||||||
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Title | HIV-1 PROTEASE COMPLEXED WITH MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 6 | ||||||
Components | RETROPEPSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / COMPLEX (ACID PROTEINASE-PEPTIDE) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / 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 / establishment of integrated proviral latency ...symbiont-mediated activation of host apoptosis / 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 / 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 / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.85 Å | ||||||
Authors | Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D.R. ...Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D.R. / Reid, R.C. / Fairlie, D.P. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease. Authors: Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D.R. / Reid, R.C. / 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 | 1b6m.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b6m.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b6m_validation.pdf.gz | 809.2 KB | Display | wwPDB validaton report |
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Full document | 1b6m_full_validation.pdf.gz | 810.8 KB | Display | |
Data in XML | 1b6m_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1b6m_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b6m ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b6m | HTTPS FTP |
-Related structure data
Related structure data | 1b6jC 1b6kC 1b6lC 1b6pC 1z1hC 1z1rC 1cpiS 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: 10765.687 Da / Num. of mol.: 2 Mutation: GLN7LYS, LEU33ILE, CYS67ABA, CYS95ABA, GLN107LYS, LEU133ILE, CYS167ABA, CYS195ABA Source method: isolated from a natural source / Details: CYS RESIDUES REPLACED WITH ABA / Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus / 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 / | |
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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: 2.18 Å3/Da / Density % sol: 43.46 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 0.1 M ACETATE BUFFER PH 5.5 AND 30-60% AMMONIUM SULFATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: the enzyme/inhibitor solution was mixed in a 1:1 ratio with precipitant solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1995 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 17002 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.046 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.76→1.82 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.276 / % possible all: 71 |
Reflection | *PLUS % possible obs: 87.5 % / Num. measured all: 52836 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 71.2 % / Rmerge(I) obs: 0.276 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1CPI Resolution: 1.85→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.96 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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