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Yorodumi- PDB-1qhi: HERPES SIMPLEX VIRUS TYPE-I THYMIDINE KINASE COMPLEXED WITH A NOV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qhi | ||||||
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Title | HERPES SIMPLEX VIRUS TYPE-I THYMIDINE KINASE COMPLEXED WITH A NOVEL NON-SUBSTRATE INHIBITOR, 9-(4-HYDROXYBUTYL)-N2-PHENYLGUANINE | ||||||
Components | PROTEIN (THYMIDINE KINASE) | ||||||
Keywords | TRANSFERASE / TRANSFERASE (PHOSPHOTRANSFERASE) THYMIDINE / TRANSFERASE (PHOSPHOTRANSFERASE) THYMIDINE KINASE / VIRIDAE / DS-DNA ENVELOPED VIRUSES / HERPESVIRIDAE / ALPHAHERPESVIRINAE NOVEL INHIBITOR | ||||||
Function / homology | Function and homology information TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Herpes simplex virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å | ||||||
Authors | Bennett, M.S. / Wien, F. / Champness, J.N. / Batuwangala, T. / Rutherford, T. / Summers, W.C. / Sun, H. / Wright, G. / Sanderson, M.R. | ||||||
Citation | Journal: FEBS Lett. / Year: 1999 Title: Structure to 1.9 A resolution of a complex with herpes simplex virus type-1 thymidine kinase of a novel, non-substrate inhibitor: X-ray crystallographic comparison with binding of aciclovir. Authors: Bennett, M.S. / Wien, F. / Champness, J.N. / Batuwangala, T. / Rutherford, T. / Summers, W.C. / Sun, H. / Wright, G. / Sanderson, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qhi.cif.gz | 135.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qhi.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qhi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1qhi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1qhi_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 1qhi_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/1qhi ftp://data.pdbj.org/pub/pdb/validation_reports/qh/1qhi | HTTPS FTP |
-Related structure data
Related structure data | 2ki5C 1kimS S: Starting model for refinement C: citing same article (ref.) |
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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: 39889.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 9-(4-HYDROXYBUTYL)-N2-PHENYLGUANINE Source: (gene. exp.) Herpes simplex virus (type 1 / strain 17) Genus: Simplexvirus / Species: Human herpesvirus 1 / Strain: 17 / Plasmid: PT7 HSVTK / Gene (production host): TK / Production host: Escherichia coli (E. coli) / Strain (production host): SY211 References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase #2: Chemical | #3: Chemical | #4: 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: 2.23 Å3/Da / Density % sol: 44.8 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PUBLISHED IN BENNETT, M.S. ET AL. FEBS LETT., VOL.443 (1999) 121-125, pH 7.5 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusionDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: MIRRORS |
Radiation | Monochromator: OTWINOWSKI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→16 Å / Num. obs: 55222 / % possible obs: 92 % / Observed criterion σ(I): 3 / Redundancy: 2.5 % / Biso Wilson estimate: 20.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.87→1.93 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.36 / % possible all: 89.1 |
Reflection | *PLUS Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 89.1 % / Rmerge(I) obs: 0.36 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1KIM Resolution: 1.9→12 Å / Isotropic thermal model: INDIVIDUAL B-FACTOR REFINEMENT / Cross valid method: FREE R / σ(F): 3 / Details: NCS RESTRAINTS NOT USED IN FINAL CYCLES.
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NCS RESTRAINT NOT USED IN FINAL REFINEMENT STAGES. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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