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Open data
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Basic information
Entry | Database: PDB / ID: 2ocp | |||||||||
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Title | Crystal Structure of Human Deoxyguanosine Kinase | |||||||||
![]() | Deoxyguanosine kinase | |||||||||
![]() | TRANSFERASE / PROTEIN-NUCLEOTIDE COMPLEX | |||||||||
Function / homology | ![]() dGTP metabolic process / purine deoxyribonucleoside metabolic process / guanosine metabolic process / purine-containing compound salvage / 2'-deoxyadenosine kinase / deoxyguanosine kinase / deoxyguanosine kinase activity / deoxyadenosine kinase activity / ATP biosynthetic process / Purine salvage ...dGTP metabolic process / purine deoxyribonucleoside metabolic process / guanosine metabolic process / purine-containing compound salvage / 2'-deoxyadenosine kinase / deoxyguanosine kinase / deoxyguanosine kinase activity / deoxyadenosine kinase activity / ATP biosynthetic process / Purine salvage / deoxynucleoside kinase activity / mitochondrial ATP synthesis coupled electron transport / negative regulation of neuron projection development / mitochondrial matrix / protein phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Johansson, K. / Ramaswamy, S. / Ljungkrantz, C. / Knecht, W. / Piskur, J. / Munch-Petersen, B. / Eriksson, S. / Eklund, H. | |||||||||
![]() | ![]() Title: Structural Basis for Substrate Specificities of Cellular Deoxyribonucleoside Kinases. Authors: Johansson, K. / Ramaswamy, S. / Ljungkrantz, C. / Knecht, W. / Piskur, J. / Munch-Petersen, B. / Eriksson, S. / Eklund, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 389.7 KB | Display | ![]() |
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PDB format | ![]() | 321.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 77.4 KB | Display | |
Data in CIF | ![]() | 92.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j90SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28319.338 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-DTP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, AMMONIUM ACETATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 11, 1999 |
Radiation | Monochromator: DIAMOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 61311 / % possible obs: 97.5 % / Observed criterion σ(I): 2.2 / Redundancy: 3.5 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.2 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J90 Resolution: 2.8→30 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: THE STRUCTURE IS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY. ONLY MOLECULE A WAS BUILT INTO AVERAGE MAPS AND THE OTHER SEVEN (B-H) MOLECULES WERE GENERATED ACCORDING TO THE NCS ...Details: THE STRUCTURE IS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY. ONLY MOLECULE A WAS BUILT INTO AVERAGE MAPS AND THE OTHER SEVEN (B-H) MOLECULES WERE GENERATED ACCORDING TO THE NCS SYMMETRY AND ARE THUS IDENTICAL TO MOLECULE A.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.88 Å2 / ksol: 0.29 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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