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Yorodumi- PDB-1htf: X-RAY CRYSTALLOGRAPHIC STUDIES OF A SERIES OF PENICILLIN-DERIVED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1htf | ||||||
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Title | X-RAY CRYSTALLOGRAPHIC STUDIES OF A SERIES OF PENICILLIN-DERIVED ASYMMETRIC INHIBITORS OF HIV-1 PROTEASE | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE(ACID 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 / 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: 2.2 Å | ||||||
Authors | Jhoti, H. / Wonacott, A. / Murray-Rust, P. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease. Authors: Jhoti, H. / Singh, O.M. / Weir, M.P. / Cooke, R. / Murray-Rust, P. / Wonacott, A. #1: Journal: J.Med.Chem. / Year: 1993 Title: A Series of Penicillin-Derived C2-Symmetric Inhibitors of HIV-1 Proteinase: Structural and Modeling Studies Authors: Wonacott, A. / Cooke, R. / Hayes, F.R. / Hayes, M.M. / Jhoti, H. / Mcmeekin, P. / Mistry, A. / Murray-Rust, P. / Singh, O.M.P. / Weir, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1htf.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1htf.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 1htf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/1htf ftp://data.pdbj.org/pub/pdb/validation_reports/ht/1htf | 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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Atom site foot note | 1: GLY B 52 - PHE B 53 OMEGA = 216.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 10803.756 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: P03366 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | GR126045 IS (2R,4S)-2-[(R)-BENZYLCARBAMOYL- PHENYLACETYLAMINO-METHYL]-5,5-DIMETHYL-THIAZOLIDINE-4- ...GR126045 IS (2R,4S)-2-[(R)-BENZYLCARB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.08 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 5.4 / PH range high: 3.4 | ||||||||||||||||||||||||
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: 2.2 Å / Num. obs: 8469 / % possible obs: 87 % / Rmerge(I) obs: 0.077 |
-Processing
Software |
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 Details: RESIDUES PHE A 53 AND PHE B 53 HAVE ALTERNATE CONFORMATIONS FOR THE PHENYL RING. THE CONFORMATIONS ARE EXHIBITED BY THE TWO SUBUNITS.
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 / Rfactor Rwork: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3 |