[English] 日本語
Yorodumi- PDB-1e2h: The nucleoside binding site of Herpes simplex type 1 thymidine ki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e2h | ||||||
---|---|---|---|---|---|---|---|
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1e2h.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1e2h.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2h ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2h | HTTPS FTP |
---|
-Related structure data
Related structure data | 1e2iC 1e2jC 1vtkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92857, -0.31386, -0.19811), Vector: Details | THE STRONG CRYSTAL PACKING GENERATED USING X , 1-Y, -Z GIVESCHAIN A TO CHAIN A (SYMMETRY RELATED) CONTACTS. | |
-Components
#1: Protein | Mass: 35779.086 Da / Num. of mol.: 2 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.16 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: LITHIUM SULPHATE, HEPES, DTT, 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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9057 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 56856 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.231 / % possible all: 99 |
Reflection | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS Rmerge(I) obs: 0.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VTK Resolution: 1.9→20 Å / SU B: 1.9 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.215 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |