+Open data
-Basic information
Entry | Database: PDB / ID: 1hxb | ||||||
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Title | HIV-1 proteinase complexed with RO 31-8959 | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / ASPARTYL PROTEASE | ||||||
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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / host multivesicular body / protein processing / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / peptidase activity / 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 / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Graves, B.J. / Hatada, M.H. / Crowther, R.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1991 Title: Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere. Authors: Krohn, A. / Redshaw, S. / Ritchie, J.C. / Graves, B.J. / Hatada, M.H. #1: Journal: Science / Year: 1990 Title: Rational Design of Peptide-Based HIV Proteinase Inhibitors Authors: Roberts, N.A. / Martin, J.A. / Kinchington, D. / Broadhurst, A.V. / Craig, J.C. / Duncan, I.B. / Galpin, S.A. / Handa, B.K. / Kay, J. / Krohn, A. / Lambert, R.W. / Merrett, J.H. / Mills, J.S. ...Authors: Roberts, N.A. / Martin, J.A. / Kinchington, D. / Broadhurst, A.V. / Craig, J.C. / Duncan, I.B. / Galpin, S.A. / Handa, B.K. / Kay, J. / Krohn, A. / Lambert, R.W. / Merrett, J.H. / Mills, J.S. / Parkes, K.E.B. / Redshaw, S. / Ritchie, A.J. / Taylor, D.L. / Thomas, G.J. / Machin, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hxb.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hxb.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hxb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1hxb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1hxb_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1hxb_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/1hxb ftp://data.pdbj.org/pub/pdb/validation_reports/hx/1hxb | HTTPS FTP |
-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: 10789.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (CLONE 12) Gene: POL / Variant: HXB-3 / Plasmid: PPTDELTAN / Gene (production host): POL / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, HIV-1 retropepsin #2: Chemical | ChemComp-ROC / ( | #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR ROC IS A HYDROXYETH | Sequence details | SEE REFERENCE R.A.KRAMER,M.D.SCHABER, A.M.SKALKA,K.GANGULY, F.WONG-STAAL,E.P.REDDY (1986) SCIENCE ...SEE REFERENCE R.A.KRAMER,M.D.SCHABER, A.M.SKALKA,K.GANGULY, F.WONG-STAAL,E.P.REDDY (1986) SCIENCE 231, 1580-1584. | Source details | DETAILS OF THE CLONING AND EXPRESSION ARE PUBLISHED [M.C. GRAVES, J.J. LIM, E.P. HEIMER & R.A. ...DETAILS OF THE CLONING AND EXPRESSION | |
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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: 2.17 Å3/Da / Density % sol: 43.4 % Description: THE DATA REDUNDANCY IS 4.6 FOR DATA TO 2.01 ANGSTROMS RESOLUTION. R MERGE IS 0.035 FOR DATA TO 2.01 ANGSTROMS RESOLUTION. THE NUMBER OF UNIQUE REFLECTIONS IS 11337 TO 2.01 ANGSTROMS RESOLUTION. |
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Crystal grow | *PLUS |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: ADSC / Detector: AREA DETECTOR / Date: Sep 15, 1990 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | % possible obs: 91.6 % / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Resolution: 2.3→10 Å / σ(F): 0 Details: THE STEREOCHEMICAL PARAMETERS USED WERE THOSE DISTRIBUTED WITH VERSION 2.1 OF X-PLOR. THE ASYMMETRIC UNIT CONSISTS OF THE PROTEIN DIMER AND ONE INHIBITOR MOLECULE. THE INHIBITOR HAS BEEN ...Details: THE STEREOCHEMICAL PARAMETERS USED WERE THOSE DISTRIBUTED WITH VERSION 2.1 OF X-PLOR. THE ASYMMETRIC UNIT CONSISTS OF THE PROTEIN DIMER AND ONE INHIBITOR MOLECULE. THE INHIBITOR HAS BEEN PLACED IN TWO ORIENTATIONS WITH OCCUPANCIES OF 0.56 AND 0.44 WHICH WERE CHOSEN TO MAKE THE TWO SETS OF TEMPERATURE FACTORS MORE EQUIVALENT. RESTRAINTS FROM NON-CRYSTALLOGRAPHIC SYMMETRY WERE NOT USED IN REFINEMENT.
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Displacement parameters | Biso mean: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å /
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