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Yorodumi- PDB-7hvp: X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A COMPLEX BETWEEN A SYNTHETIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7hvp | |||||||||
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Title | X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A COMPLEX BETWEEN A SYNTHETIC PROTEASE OF HUMAN IMMUNODEFICIENCY VIRUS 1 AND A SUBSTRATE-BASED HYDROXYETHYLAMINE INHIBITOR | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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 / symbiont-mediated suppression of host gene expression / 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: 2.4 Å | |||||||||
Authors | Swain, A.L. / Miller, M.M. / Green, J. / Rich, D.H. / Schneider, J. / Kent, S.B.H. / Wlodawer, A. | |||||||||
Citation | 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. / Wlodawer, A. #1: Journal: Biochemistry / Year: 1991 Title: Structure at 2.5-Angstroms Resolution of Chemically Synthesized Human Immunodeficiency Virus Type I Protease Complexed with a Hydroxyethylene-Based Inhibitor Authors: Jaskolski, M. / Tomasselli, A.G. / Sawyer, T.K. / Staples, D.G. / Heinrikson, R.L. / Schneider, J. / Kent, S.B. / Wlodawer, A. #2: 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.M. / Clawson, L. / Schneider, J. / Kent, S.B.H. #3: Journal: Science / Year: 1989 Title: Structure of Complex of Synthetic HIV-1 Protease with a Substrate-Based Inhibitor at 2.3 Angstroms Resolution Authors: Miller, M. / Schneider, J. / Sathyanarayana, B.K. / Toth, M.V. / Marshall, G.R. / Clawson, L. / Selk, L. / Kent, S.B.H. / Wlodawer, A. #4: Journal: Science / Year: 1989 Title: Molecular Modeling of the HIV-1 Protease and its Substrate Binding Site Authors: Weber, I.T. / Miller, M. / Jaskolski, M. / Leis, J. / Skalka, A.M. / Wlodawer, A. #5: Journal: Nature / Year: 1989 Title: Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family Authors: Miller, M. / Jaskolski, M. / Rao, J.K.M. / Leis, J. / Wlodawer, A. #6: Journal: Cell(Cambridge,Mass.) / Year: 1988 Title: Enzymatic Activity of a Synthetic 99 Residue Protein Corresponding to the Putative HIV-1 Protease Authors: Schneider, J. / Kent, S.B.H. | |||||||||
History |
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Remark 700 | SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTIPARALLEL BETA-SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7hvp.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7hvp.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 7hvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/7hvp ftp://data.pdbj.org/pub/pdb/validation_reports/hv/7hvp | 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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Atom site foot note | 1: RESIDUE PRO C 6 IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 10764.636 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 #2: Protein/peptide | | #3: Water | ChemComp-HOH / | Compound details | THE PEPTIDE BOND BEFORE THE PRO SUBCOMPONENT IN THE INHIBITOR IS REPLACED BY A HYDROXYETHYLAMINE ...THE PEPTIDE BOND BEFORE THE PRO SUBCOMPONE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.04 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 5398 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.089 |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.4→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. reflection obs: 5398 / Rfactor obs: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.1 Å2 |