+Open data
-Basic information
Entry | Database: PDB / ID: 2i6a | ||||||
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Title | Human Adenosine Kinase in Complex With 5'-Deoxy-5-Iodotubercidin | ||||||
Components | Adenosine kinase | ||||||
Keywords | TRANSFERASE / protein-ligand complex / 5'-deoxy-5-iodotubercidin | ||||||
Function / homology | Function and homology information dATP biosynthetic process / adenosine kinase / adenosine kinase activity / dAMP salvage / ribonucleoside monophosphate biosynthetic process / deoxyadenosine kinase activity / Ribavirin ADME / GMP salvage / Purine salvage / AMP salvage ...dATP biosynthetic process / adenosine kinase / adenosine kinase activity / dAMP salvage / ribonucleoside monophosphate biosynthetic process / deoxyadenosine kinase activity / Ribavirin ADME / GMP salvage / Purine salvage / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Muchmore, S.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Crystal structures of human adenosine kinase inhibitor complexes reveal two distinct binding modes. Authors: Muchmore, S.W. / Smith, R.A. / Stewart, A.O. / Cowart, M.D. / Gomtsyan, A. / Matulenko, M.A. / Yu, H. / Severin, J.M. / Bhagwat, S.S. / Lee, C.H. / Kowaluk, E.A. / Jarvis, M.F. / Jakob, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i6a.cif.gz | 283.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i6a.ent.gz | 230.9 KB | Display | PDB format |
PDBx/mmJSON format | 2i6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/2i6a ftp://data.pdbj.org/pub/pdb/validation_reports/i6/2i6a | HTTPS FTP |
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-Related structure data
-Links
-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: 38755.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADK / Production host: Escherichia coli (E. coli) / References: UniProt: Q5VXR3, UniProt: P55263*PLUS #2: Chemical | ChemComp-5I5 / #3: 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: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 4000, 0.1 M MgCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 41591 / Num. obs: 35353 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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