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- PDB-4c6p: 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: 4c6p | |||||||||
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Title | Crystal structure of the dihydroorotase domain of human CAD C1613S mutant in apo-form 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 / extracellular exosome / zinc ion binding / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm 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 | ![]() | 237.1 KB | Display | ![]() |
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PDB format | ![]() | 192.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 447.8 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 29.6 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 ![]() 4c6qC 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
#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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#2: Chemical | #3: Chemical | ChemComp-FMT / #4: 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: Feb 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28306 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→19.88 Å / Num. obs: 61664 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 18.99 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.52→1.56 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 90.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4C6C Resolution: 1.518→19.879 Å / SU ML: 0.11 / σ(F): 0.87 / Phase error: 13.23 / 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: 1.518→19.879 Å
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Refine LS restraints |
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LS refinement shell |
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