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- PDB-8pbp: Mutant R1785C of the dihydroorotase domain of human CAD protein b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pbp | ||||||||||||
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Title | Mutant R1785C of the dihydroorotase domain of human CAD protein bound to the substrate carbamoyl aspartate | ||||||||||||
![]() | CAD protein![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | del Cano-Ochoa, F. / Ramon-Maiques, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.3 KB | Display | ![]() |
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PDB format | ![]() | 173.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8pbeC ![]() 8pbgC ![]() 8pbhC ![]() 8pbiC ![]() 8pbjC ![]() 8pbkC ![]() 8pbmC ![]() 8pbnC ![]() 8pbqC ![]() 8pbrC ![]() 8pbsC ![]() 8pbtC ![]() 8pbuC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 39640.375 Da / Num. of mol.: 1 / Mutation: R1785C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P27708, ![]() ![]() ![]() |
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-Non-polymers , 5 types, 252 molecules ![](data/chem/img/NCD.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/DOR.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/DOR.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NCD / | ||||||
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#3: Chemical | ![]() #4: Chemical | ChemComp-DOR / ( | #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES pH 7, 2.8 M sodium formate, 2 mM carbamoyl aspartate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.54→48.72 Å / Num. obs: 59225 / % possible obs: 98.74 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.19 |
Reflection shell | Resolution: 1.54→1.595 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 5377 / CC1/2: 0.568 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→48.72 Å
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Refine LS restraints |
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LS refinement shell |
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