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- PDB-2j2c: Crystal structure of Human Cytosolic 5'-Nucleotidase II (NT5C2, cN-II) -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j2c | ||||||
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Title | Crystal structure of Human Cytosolic 5'-Nucleotidase II (NT5C2, cN-II) | ||||||
![]() | CYTOSOLIC PURINE 5'-NUCLEOTIDASE | ||||||
![]() | HYDROLASE / CYTOSOLIC 5-PRIME NUCLEOTIDASE II / ALLOSTERIC ENZYME / GMP- IMP SPECIFIC NUCLEOTIDASE / HIGH KM 5-PRIME NUCLEOTIDASE / CN- II / NT5C2 / CYTOSOLIC PURINE 5- PRIME NUCLEOTIDASE | ||||||
Function / homology | ![]() nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Ribavirin ADME / IMP metabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. ...Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Karlberg, T. / Kotenyova, T. / Loppnau, P. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. | ||||||
![]() | ![]() Title: Crystal Structure of Human Cytosolic 5'- Nucleotidase II: Insights Into Allosteric Regulation and Substrate Recognition Authors: Wallden, K. / Stenmark, P. / Nyman, T. / Flodin, S. / Graslund, S. / Loppnau, P. / Bianchi, V. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.3 KB | Display | ![]() |
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PDB format | ![]() | 93.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 451 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cn1C ![]() 2jc9C ![]() 2jcmC ![]() 2jgaC ![]() 2bdeS 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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Unit cell |
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Components
#1: Protein | Mass: 64088.930 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-536 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-GOL / | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Sequence details | OUR CONSTRUCT CONTAINS RESIDUES 1-536 OUT OF THE 561 AMINO ACIDS. ADDITIONALLY IT CONTAINS AN N- ...OUR CONSTRUCT CONTAINS RESIDUES 1-536 OUT OF THE 561 AMINO ACIDS. ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Details: 1.8 M MG2SO4 0.1 M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 22, 2006 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→91.29 Å / Num. obs: 39212 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 11.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BDE Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.989 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 3-400 AND 417-488 OUT OF 536 RESIDUES ARE MODELLED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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