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- PDB-5k9c: Crystal structure of human dihydroorotate dehydrogenase with ML390 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k9c | ||||||
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Title | Crystal structure of human dihydroorotate dehydrogenase with ML390 | ||||||
![]() | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Oxidoreductase / alpha/beta barrel / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lewis, T.A. / Sykes, D.B. / Law, J.M. / Munoz, B. / Scadden, D.T. / Rustiguel, J.K. / Nonato, M.C. / Schreiber, S.L. | ||||||
![]() | ![]() Title: Development of ML390: A Human DHODH Inhibitor That Induces Differentiation in Acute Myeloid Leukemia. Authors: Lewis, T.A. / Sykes, D.B. / Law, J.M. / Munoz, B. / Rustiguel, J.K. / Nonato, M.C. / Scadden, D.T. / Schreiber, S.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.3 KB | Display | ![]() |
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PDB format | ![]() | 187.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k9dC ![]() 1d3gS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39943.613 Da / Num. of mol.: 1 / Fragment: residues 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 8 types, 351 molecules ![](data/chem/img/FNR.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/MLJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/MLJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FNR / | ||||||||
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#3: Chemical | ChemComp-ORO / | ||||||||
#4: Chemical | ChemComp-MLJ / ~{ | ||||||||
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 0.1 M sodium acetate trihydrate pH 4.8 1.9 M ammonium sulfate 30% (v/v) glycerol PH range: 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 10, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double-crystal monochromator and toroidal bendable mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.66→25.952 Å / Num. obs: 67579 / % possible obs: 99.8 % / Redundancy: 15.1 % / Biso Wilson estimate: 14.33 Å2 / CC1/2: 0.998 / Rsym value: 0.097 / Net I/σ(I): 18.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1D3G Resolution: 1.66→25.952 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 12.65 Details: THE AUTHORS STATE THAT ELECTRON DENSITY ANALYSIS REVEALED THAT THE MAIN CHAIN HAD A DOUBLE CONFORMATION ( FROM RESIDUE 211 TO 226), DUE TO ITS EXPECTED FLEXIBILITY (AS A CATALYTIC LOOP). ...Details: THE AUTHORS STATE THAT ELECTRON DENSITY ANALYSIS REVEALED THAT THE MAIN CHAIN HAD A DOUBLE CONFORMATION ( FROM RESIDUE 211 TO 226), DUE TO ITS EXPECTED FLEXIBILITY (AS A CATALYTIC LOOP). VAL213 SHOWED A VERY CLEAR ELECTRON DENSITY IN CONFORMATION B, BUT IN CONTRAST, CONFORMATION A WAS DOMINANT FOR RESIDUES FROM 214 TO 218. THE VAL213 CONFORMER AND THE SER214 A CONFORMER WERE CONFLICTING AS A CONSEQUENCE OF THE DIFFERENT LOOP ARRANGEMENTS (OPEN AND CLOSED CONFORMATIONS). TAKING ALL THESE INTO ACCOUNT, THE AUTHORS STATE THAT THE VAL213 DOUBLE CONFORMATION IS THE SOLUTION THAT BETTER FITS THE DATASET AND THEREFORE, VAL213 (B CONFORMER) AND SER214 (A CONFORMER) ARE NOT LINKED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.79 Å2 / Biso mean: 23.5645 Å2 / Biso min: 5.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.66→25.952 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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