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- PDB-4c6q: Crystal structure of the dihydroorotase domain of human CAD C1613... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c6q | |||||||||
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Title | Crystal structure of the dihydroorotase domain of human CAD C1613S mutant bound to substrate at pH 7.0 | |||||||||
![]() | CAD PROTEIN | |||||||||
![]() | HYDROLASE / DE NOVO PYRIMIDINE BIOSYNTHESIS / AMIDOHYDROLASE SUPERFAMILY / METALLOENZYME / ZINC BINDING / HISTIDINATE ANION | |||||||||
Function / homology | ![]() aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase ...aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase / aspartate carbamoyltransferase activity / dihydroorotase activity / Pyrimidine biosynthesis / glutaminase activity / UTP biosynthetic process / UDP biosynthetic process / response to caffeine / response to testosterone / glutamine metabolic process / response to amine / response to starvation / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to epidermal growth factor stimulus / lactation / xenobiotic metabolic process / liver development / cell projection / female pregnancy / peptidyl-threonine phosphorylation / response to insulin / terminal bouton / nuclear matrix / heart development / protein autophosphorylation / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ramon-Maiques, S. / Lallous, N. / Grande-Garcia, A. | |||||||||
![]() | ![]() Title: Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad. Authors: Grande-Garcia, A. / Lallous, N. / Diaz-Tejada, C. / Ramon-Maiques, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249 KB | Display | ![]() |
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PDB format | ![]() | 203.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.5 KB | Display | ![]() |
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Full document | ![]() | 480.2 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4by3C ![]() 4c6bC ![]() 4c6cSC ![]() 4c6dC ![]() 4c6eC ![]() 4c6fC ![]() 4c6iC ![]() 4c6jC ![]() 4c6kC ![]() 4c6lC ![]() 4c6mC ![]() 4c6nC ![]() 4c6oC ![]() 4c6pC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42899.953 Da / Num. of mol.: 1 / Fragment: RESIDUES 1456-1846 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 439 molecules ![](data/chem/img/ORO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NCD.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NCD.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ORO / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-NCD / | #5: Chemical | ChemComp-FMT / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→47.08 Å / Num. obs: 47725 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.66→1.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4C6C Resolution: 1.659→47.077 Å / SU ML: 0.17 / σ(F): 1.18 / Phase error: 16.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.659→47.077 Å
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Refine LS restraints |
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LS refinement shell |
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