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Yorodumi- PDB-1e2j: The nucleoside binding site of Herpes simplex type 1 thymidine ki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e2j | ||||||
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Title | The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography | ||||||
Components | THYMIDINE KINASE | ||||||
Keywords | TRANSFERASE / ADENINE ANALOG / ENZYME-PRODRUG GENE THERAPY / NUCLEOSIDE- BINDING / THYMIDINE KINASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Vogt, J. / Scapozza, L. / Schulz, G.E. | ||||||
Citation | Journal: Proteins: Struct.,Funct., Genet. / Year: 2000 Title: Nucleoside Binding Site of Herpes Simplex Type 1 Thymidine Kinase Analyzed by X-Ray Crystallography Authors: Vogt, J. / Perozzo, R. / Pautsch, A. / Prota, A. / Schelling, P. / Pilger, B. / Folkers, G. / Scapozza, L. / Schulz, G.E. #1: Journal: FEBS Lett. / Year: 1995 Title: The Three-Dimensional Structure of Thymidine Kinase from Herpes Simplex Virus Type 1 Authors: Wild, K. / Bohner, T. / Aubry, A. / Folkers, G. / Schulz, G.E. #2: Journal: Nat.Struct.Biol. / Year: 1995 Title: Crystal Structures of the Thymidine Kinase from Herpes Simplex Virus Type-1 in Complex with Deoxythymidine and Ganciclovir Authors: Brown, D.G. / Visse, R. / Sandhu, G. / Davies, A. / Rizkallah, P.J. / Melitz, C. / Summers, W.C. / 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 | 1e2j.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e2j.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 1e2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2j ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2j | HTTPS FTP |
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-Related structure data
Related structure data | 1e2hC 1e2iC 1vtkS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92776, -0.32039, -0.19133), Vector: Details | THE STRONG CRYSTAL PACKING GENERATED USING X , 1-Y, -Z GIVESCHAIN A TO CHAIN A (SYMMETRY RELATED) CONTACTS. | |
-Components
#1: Protein | Mass: 35765.059 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HERPES SIMPLEX VIRUS (TYPE 1/STRAIN 17) Strain: 17 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CHAIN A AND B ENGINEERED | |
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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: 2.53 Å3/Da / Density % sol: 51.36 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: LITHIUM SULPHATE, HEPES, DTT, DT, pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, sitting drop / PH range low: 8 / PH range high: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MULTIWIRE SIEMENS / Detector: AREA DETECTOR / Date: Nov 24, 1998 |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 23273 / % possible obs: 92 % / Redundancy: 2.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.17 / % possible all: 92 |
Reflection | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VTK Resolution: 2.5→20 Å / SU B: 6.64 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.647 / ESU R Free: 0.325
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Displacement parameters | Biso mean: 28.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.212 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |