+Open data
-Basic information
Entry | Database: PDB / ID: 1e2m | ||||||
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Title | HPT + HMTT | ||||||
Components | THYMIDINE KINASE | ||||||
Keywords | TRANSFERASE | ||||||
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: 2.2 Å | ||||||
Authors | Vogt, J. / Scapozza, L. / Schulz, G.E. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: The Effect of Substrate Binding on the Conformation and Structural Stability of Herpes Simplex Virus Type 1 Thymidine Kinase Authors: Wurth, C. / Kessler, U. / Vogt, J. / Schulz, G.E. / Folkers, G. / Scapozza, L. #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 | 1e2m.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e2m.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 1e2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e2m_validation.pdf.gz | 458.9 KB | Display | wwPDB validaton report |
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Full document | 1e2m_full_validation.pdf.gz | 471.7 KB | Display | |
Data in XML | 1e2m_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 1e2m_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2m ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2m | HTTPS FTP |
-Related structure data
Related structure data | 1e2nC 1e2pC 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: (-0.92428, -0.32871, -0.19407), 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: 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: 2.53 Å3/Da / Density % sol: 51.3 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: LITHIUM SULFATE, HEPES, DTT, pH 7.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Prota, A., (2000) Biochemistry, 39, 9597. | ||||||||||||||||||||||||||||||||||||
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 RU2HC / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 36554 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.49 / % possible all: 97 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTR 1VTK Resolution: 2.2→20 Å / SU B: 3.5 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.22
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Displacement parameters | Biso mean: 28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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