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Yorodumi- PDB-8pbt: Mutant K1482M of the dihydroorotase domain of human CAD protein b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pbt | ||||||||||||
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Title | Mutant K1482M of the dihydroorotase domain of human CAD protein bound to the substrate dihydroorotate | ||||||||||||
Components | CAD protein | ||||||||||||
Keywords | HYDROLASE / Nucleotide metabolism / de novo pyrimidine synthesis / CAD disease / multienzymatic protein / zinc / carboxylated lysine / BIOSYNTHETIC PROTEIN | ||||||||||||
Function / homology | Function and homology information 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 / UDP biosynthetic process / glutaminase activity / UTP biosynthetic process / response to caffeine / glutamine metabolic process / response to starvation / response to amine / response to testosterone / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / animal organ regeneration / lactation / cellular response to epidermal growth factor stimulus / 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 / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||||||||
Authors | del Cano-Ochoa, F. / Ramon-Maiques, S. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: J Inherit Metab Dis / Year: 2023 Title: Beyond genetics: Deciphering the impact of missense variants in CAD deficiency. Authors: Del Cano-Ochoa, F. / Ng, B.G. / Rubio-Del-Campo, A. / Mahajan, S. / Wilson, M.P. / Vilar, M. / Rymen, D. / Sanchez-Pintos, P. / Kenny, J. / Ley Martos, M. / Campos, T. / Wortmann, S.B. / ...Authors: Del Cano-Ochoa, F. / Ng, B.G. / Rubio-Del-Campo, A. / Mahajan, S. / Wilson, M.P. / Vilar, M. / Rymen, D. / Sanchez-Pintos, P. / Kenny, J. / Ley Martos, M. / Campos, T. / Wortmann, S.B. / Freeze, H.H. / Ramon-Maiques, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pbt.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pbt.ent.gz | 187.7 KB | Display | PDB format |
PDBx/mmJSON format | 8pbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pbt_validation.pdf.gz | 806 KB | Display | wwPDB validaton report |
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Full document | 8pbt_full_validation.pdf.gz | 806 KB | Display | |
Data in XML | 8pbt_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 8pbt_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pbt ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pbt | HTTPS FTP |
-Related structure data
Related structure data | 8pbeC 8pbgC 8pbhC 8pbiC 8pbjC 8pbkC 8pbmC 8pbnC 8pbpC 8pbqC 8pbrC 8pbsC 8pbuC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 39696.445 Da / Num. of mol.: 1 / Mutation: K1482M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M-huDHO-K1482M / Cell (production host): epithelial-like / Cell line (production host): HEK293S GnTI / Organ (production host): Embryo / Production host: Homo sapiens (human) / Tissue (production host): Kidney References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase |
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-Non-polymers , 5 types, 351 molecules
#2: Chemical | ChemComp-GOL / | ||||
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#3: Chemical | ChemComp-DOR / ( | ||||
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-FMT / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM HEPES pH 6.5, 2.7 M sodium formate, 2 mM dihydroorotate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→79.36 Å / Num. obs: 424906 / % possible obs: 87.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.56 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.97 |
Reflection shell | Resolution: 1.435→1.486 Å / Mean I/σ(I) obs: 1.61 / Num. unique obs: 7254 / CC1/2: 0.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→79.36 Å / SU ML: 0.1603 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0257 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→79.36 Å
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Refine LS restraints |
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LS refinement shell |
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