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- PDB-6dd3: Crystal structure of the double mutant (D52N/D407A) of NT5C2-537X... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dd3 | |||||||||||||||
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Title | Crystal structure of the double mutant (D52N/D407A) of NT5C2-537X in the active state | |||||||||||||||
![]() | Cytosolic purine 5'-nucleotidase | |||||||||||||||
![]() | HYDROLASE | |||||||||||||||
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 | ![]() ![]() ![]() | |||||||||||||||
![]() | Forouhar, F. / Dieck, C.L. / Tzoneva, G. / Carpenter, Z. / Ambesi-Impiombato, A. / Sanchez-Martin, M. / Kirschner-Schwabe, R. / Lew, S. / Seetharaman, J. / Ferrando, A.A. / Tong, L. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Authors: Dieck, C.L. / Tzoneva, G. / Forouhar, F. / Carpenter, Z. / Ambesi-Impiombato, A. / Sanchez-Martin, M. / Kirschner-Schwabe, R. / Lew, S. / Seetharaman, J. / Tong, L. / Ferrando, A.A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224 KB | Display | ![]() |
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PDB format | ![]() | 178.2 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 | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ddbC ![]() 6ddcC ![]() 6ddhC ![]() 6ddkC ![]() 6ddlC ![]() 6ddoC ![]() 6ddqC ![]() 6ddxC ![]() 6ddyC ![]() 6ddzC ![]() 6de0C ![]() 6de1C ![]() 6de2C ![]() 6de3C 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: 62010.703 Da / Num. of mol.: 1 / Fragment: residues 1-536 / Mutation: D52N, D407A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 2 M Ammonium sulfate and 5% 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→48.82 Å / Num. obs: 69431 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 29.58 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.91 / Rpim(I) all: 0.02 / Rrim(I) all: 0.93 / Rsym value: 0.92 / Χ2: 0.977 / Net I/av σ(I): 25.1 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3435 / CC1/2: 0.96 / Rpim(I) all: 0.14 / Rrim(I) all: 0.5 / Rsym value: 0.51 / Χ2: 0.65 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→38.252 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.0213 Å / Origin y: 38.8669 Å / Origin z: 19.2991 Å
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Refinement TLS group | Selection details: all |