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Yorodumi- PDB-4phv: X-RAY CRYSTAL STRUCTURE OF THE HIV PROTEASE COMPLEX WITH L-700,41... -
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-Basic information
Entry | Database: PDB / ID: 4phv | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF THE HIV PROTEASE COMPLEX WITH L-700,417, AN INHIBITOR WITH PSEUDO C2 SYMMETRY | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE(ASPARTIC PROTEINASE) | ||||||
Function / homology | Function and homology information : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Bone, R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1991 Title: X-Ray Crystal Structure of the HIV Protease Complex with L-700,417, an Inhibitor with Pseudo C2 Symmetry Authors: Bone, R. / Vacca, J.P. / Anderson, P.S. / Holloway, M.K. #1: Journal: Science / Year: 1990 Title: Design, Activity, and 2.8 Angstroms Crystal Structure of a C2 Symmetric Inhibitor Complexed to HIV-1 Protease Authors: Erickson, J. / Neidhart, D.J. / Van Drie, J. / Kempf, D.J. / Wang, X.C. / Norbeck, D.W. / Plattner, J.J. / Rittenhouse, J.W. / Turon, M. / Wideburg, N. / Kohlbrenner, W.E. / Simmer, R. / ...Authors: Erickson, J. / Neidhart, D.J. / Van Drie, J. / Kempf, D.J. / Wang, X.C. / Norbeck, D.W. / Plattner, J.J. / Rittenhouse, J.W. / Turon, M. / Wideburg, N. / Kohlbrenner, W.E. / Simmer, R. / Helfrich, R. / Paul, D.A. / Knigge, M. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Crystallographic Analysis of a Complex between Human Immunodeficiency Virus Type 1 Protease and Acetyl-Pepstatin at 2.0 Angstroms Resolution Authors: Fitzgerald, P.M.D. / Mckeever, B.M. / Van Middlesworth, J.F. / Springer, J.P. / Heimbach, J.C. / Leu, C.-T. / Herber, W.K. / Dixon, R.A.F. / Darke, P.L. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990 Title: X-Ray Crystallographic Structure of a Complex between a Synthetic Protease of Human Immunodeficiency Virus 1 and a Substrate-Based Hydroxyethylamine Inhibitor Authors: Swain, A.L. / Miller, M.M. / Green, J. / Rich, D.H. / Schneider, J. / Kent, S.B.H. / Wlodawer, A. #4: Journal: Nature / Year: 1989 Title: Three-Dimensional Structure of Aspartyl Protease from Human Immunodeficiency Virus HIV-1 Authors: Navia, M.A. / Fitzgerald, P.M.D. / Mckeever, B.M. / Leu, C.-T. / Heimbach, J.C. / Herber, W.K. / Sigal, I.S. / Darke, P.L. / Springer, J.P. #5: Journal: Science / Year: 1989 Title: Conserved Folding in Retroviral Proteases: Crystal Structure of a Synthetic HIV-1 Protease Authors: Wlodawer, A. / Miller, M. / Jaskolski, M. / Sathyanarayana, B.K. / Baldwin, E. / Weber, I.T. / Selk, L. / Clawson, L. / Schneider, J. / Kent, S.B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4phv.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4phv.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 4phv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/4phv ftp://data.pdbj.org/pub/pdb/validation_reports/ph/4phv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10830.781 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: P12497 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % | |||||||||||||||
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Crystal grow | *PLUS pH: 5.4 / Method: vapor diffusion / Details: macro-seeding | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.07 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection all: 12981 / σ(F): 0 / Rfactor all: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |