+Open data
-Basic information
Entry | Database: PDB / ID: 1dmp | ||||||
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Title | STRUCTURE OF HIV-1 PROTEASE COMPLEX | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | ASPARTYL PROTEINASE / AIDS / POLYPROTEIN / HYDROLASE / ASPARTYL PROTEASE / ACID PROTEASE / RNA-DIRECTED DNA POLYMERASE / ENDONUCLEASE | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase 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 / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Chang, C.-H. | ||||||
Citation | Journal: Chem.Biol. / Year: 1996 Title: Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450. Authors: Hodge, C.N. / Aldrich, P.E. / Bacheler, L.T. / Chang, C.H. / Eyermann, C.J. / Garber, S. / Grubb, M. / Jackson, D.A. / Jadhav, P.K. / Korant, B. / Lam, P.Y. / Maurin, M.B. / Meek, J.L. / ...Authors: Hodge, C.N. / Aldrich, P.E. / Bacheler, L.T. / Chang, C.H. / Eyermann, C.J. / Garber, S. / Grubb, M. / Jackson, D.A. / Jadhav, P.K. / Korant, B. / Lam, P.Y. / Maurin, M.B. / Meek, J.L. / Otto, M.J. / Rayner, M.M. / Reid, C. / Sharpe, T.R. / Shum, L. / Winslow, D.L. / Erickson-Viitanen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dmp.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dmp.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dmp ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dmp | HTTPS FTP |
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-Related structure data
Related structure data | 1hvrS 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: 10773.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH DMP450 OF DUPONT MERCK / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH102 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, HIV-1 retropepsin #2: Chemical | ChemComp-DMQ / [ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | pH: 5.4 / Details: pH 5.4 |
Crystal grow | *PLUS Method: other / Details: Erickson, J., (1990) Science, 249, 527. |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 12478 / % possible obs: 94 % / Rsym value: 0.071 |
Reflection | *PLUS Num. measured all: 45866 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1HVR Highest resolution: 2 Å /
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Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 2 / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |