+Open data
-Basic information
Entry | Database: PDB / ID: 1hpo | ||||||
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Title | HIV-1 PROTEASE TRIPLE MUTANT/U103265 COMPLEX | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE / ACID PROTEASE / ASPARTYL PROTEASE | ||||||
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Watenpaugh, K.D. / Janakiraman, M.N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1997 Title: Structure-based design of nonpeptidic HIV protease inhibitors: the sulfonamide-substituted cyclooctylpyramones. Authors: Skulnick, H.I. / Johnson, P.D. / Aristoff, P.A. / Morris, J.K. / Lovasz, K.D. / Howe, W.J. / Watenpaugh, K.D. / Janakiraman, M.N. / Anderson, D.J. / Reischer, R.J. / Schwartz, T.M. / Banitt, ...Authors: Skulnick, H.I. / Johnson, P.D. / Aristoff, P.A. / Morris, J.K. / Lovasz, K.D. / Howe, W.J. / Watenpaugh, K.D. / Janakiraman, M.N. / Anderson, D.J. / Reischer, R.J. / Schwartz, T.M. / Banitt, L.S. / Tomich, P.K. / Lynn, J.C. / Horng, M.M. / Chong, K.T. / Hinshaw, R.R. / Dolak, L.A. / Seest, E.P. / Schwende, F.J. / Rush, B.D. / Howard, G.M. / Toth, L.N. / Wilkinson, K.R. / Kakuk, T.J. / Johnson, C.W. / Cole, S.L. / Zaya, R.M. / Zipp, G.L. / Possert, P.L. / Dalga, R.J. / Zhong, W.-Z. / Williams, M.G. / Romines, K.R. #1: Journal: J.Med.Chem. / Year: 1995 Title: Structure-based design of sulfonamide-substituted non-peptidic HIV protease inhibitors. Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / McGrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.B. / ...Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / McGrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.B. / Zipp, G.L. / Ruwart, M.J. / Schwende, F.J. / Padbury, G.E. / Dalga, R.J. / Zhong, W.-Z. / Shiou, L. / Possert, P.L. / Rush, Bob D. / Wilkinson, Karen F. / Howard, Gina M. / Toth, L.N. / Williams, M.G. / Kakuk, T.J. / Cole, S.L. / Zaya, R.M. / Lovasz, K.D. / Morris, J.K. / Romines, K.R. / Thaisrivongs, S. / Aristoff, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hpo.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hpo.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/1hpo ftp://data.pdbj.org/pub/pdb/validation_reports/hp/1hpo | HTTPS FTP |
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-Related 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: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I 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: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-UNI / | #3: 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: 2.88 Å3/Da / Density % sol: 57.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.4 Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 10 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN/INHIBITOR COMPLEX AND THE PRECIPITANT OF 0.75, 1.0 1.5 2.0 M NACL AT PH'S 4.8, 5.0 AND 5.2 (0.1 M ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 10 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN/INHIBITOR COMPLEX AND THE PRECIPITANT OF 0.75, 1.0 1.5 2.0 M NACL AT PH'S 4.8, 5.0 AND 5.2 (0.1 M ACETATE BUFFER) AND AT PH'S 5.4, 5.6 AND 5.8 (0.1 M CITRATE BUFFER)., vapor diffusion - hanging drop PH range: 4.8-5.4, 5.0-5.6, 5.2-5.8 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 28, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 9119 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.2 / % possible all: 92.5 |
Reflection | *PLUS Num. measured all: 63195 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Software | *PLUS Name: CEDAR / Classification: refinement | ||||||||||||
Refinement | *PLUS Num. reflection all: 9119 / Rfactor obs: 0.179 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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