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- PDB-6g2n: Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6g2n | ||||||||||||
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Title | Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PAU | ||||||||||||
![]() | 5'(3')-deoxyribonucleotidase, cytosolic type | ||||||||||||
![]() | HYDROLASE / 5'-nucleotidase / dephosphorylation / phosphorylation / HAD-like / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | ![]() pyrimidine nucleotide binding / dTMP catabolic process / UMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / nucleotidase activity / dUMP catabolic process / amide catabolic process / Pyrimidine catabolism ...pyrimidine nucleotide binding / dTMP catabolic process / UMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / nucleotidase activity / dUMP catabolic process / amide catabolic process / Pyrimidine catabolism / IMP 5'-nucleotidase activity / IMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / dephosphorylation / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Pachl, P. / Rezacova, P. / Brynda, J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases Authors: Pachl, P. / Simak, O. / Budesinsky, M. / Brynda, J. / Rosenberg, I. / Rezacova, 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 | ![]() | 187 KB | Display | ![]() |
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PDB format | ![]() | 146 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6g22C ![]() 6g2lC ![]() 6g2mC ![]() 4yihS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23870.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CME is beta-mercapto ethanol covalently bound to cystein residue Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8TCD5, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8 Details: Morpheus H2, 0.1M MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol, 0.02M of each amino acid, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42.41 Å / Num. obs: 68116 / % possible obs: 87.8 % / Redundancy: 2.22 % / Biso Wilson estimate: 27.42 Å2 / CC1/2: 1 / Rrim(I) all: 0.026 / Net I/σ(I): 18.84 |
Reflection shell | Resolution: 1.4→1.49 Å / Redundancy: 2.21 % / Num. unique obs: 11048 / CC1/2: 0.7414 / Rrim(I) all: 0.556 / % possible all: 87.9 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.546
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YIH Resolution: 1.4→42.41 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.966 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0712 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.066 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.88 Å2 / Biso mean: 27.295 Å2 / Biso min: 14.5 Å2
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Refinement step | Cycle: final / Resolution: 1.4→42.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.404→1.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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