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Yorodumi- PDB-6et4: HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NOVEL INHIBITOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 6et4 | ||||||
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Title | HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NOVEL INHIBITOR | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / DHODH / CANCER / P53 ACTIVATION / PYRIMIDINE SYNTHESIS | ||||||
Function / homology | Function and homology information 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 / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Hakansson, M. / Walse, B. / Gustavsson, A.-L. / Lain, S. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Authors: Ladds, M.J.G.W. / van Leeuwen, I.M.M. / Drummond, C.J. / Chu, S. / Healy, A.R. / Popova, G. / Pastor Fernandez, A. / Mollick, T. / Darekar, S. / Sedimbi, S.K. / Nekulova, M. / Sachweh, M.C.C. ...Authors: Ladds, M.J.G.W. / van Leeuwen, I.M.M. / Drummond, C.J. / Chu, S. / Healy, A.R. / Popova, G. / Pastor Fernandez, A. / Mollick, T. / Darekar, S. / Sedimbi, S.K. / Nekulova, M. / Sachweh, M.C.C. / Campbell, J. / Higgins, M. / Tuck, C. / Popa, M. / Safont, M.M. / Gelebart, P. / Fandalyuk, Z. / Thompson, A.M. / Svensson, R. / Gustavsson, A.L. / Johansson, L. / Farnegardh, K. / Yngve, U. / Saleh, A. / Haraldsson, M. / D'Hollander, A.C.A. / Franco, M. / Zhao, Y. / Hakansson, M. / Walse, B. / Larsson, K. / Peat, E.M. / Pelechano, V. / Lunec, J. / Vojtesek, B. / Carmena, M. / Earnshaw, W.C. / McCarthy, A.R. / Westwood, N.J. / Arsenian-Henriksson, M. / Lane, D.P. / Bhatia, R. / McCormack, E. / Lain, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6et4.cif.gz | 184.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6et4.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 6et4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6et4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6et4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6et4_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6et4_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/6et4 ftp://data.pdbj.org/pub/pdb/validation_reports/et/6et4 | HTTPS FTP |
-Related structure data
Related structure data | 4oqvS S: Starting model for refinement |
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Similar structure data |
-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: 39856.535 Da / Num. of mol.: 1 Fragment: N-TERMINALLY TRUNCATED HUMAN DHODH, RESIDUES 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: U937 / Gene: DHODH / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 9 types, 273 molecules
#2: Chemical | ChemComp-FMN / | ||||||||
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#3: Chemical | ChemComp-DOR / ( | ||||||||
#4: Chemical | ChemComp-SDV / | ||||||||
#5: Chemical | ChemComp-DDQ / | ||||||||
#6: Chemical | ChemComp-ACY / #7: Chemical | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Sequence details | START AT POSITION 31 IN SEQUENCE TGDER.. ETC (FIRST TWO AA MA HAS BEEN ADDED) |
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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: 3.67 Å3/Da / Density % sol: 66.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 30% glycerol, 100 mM Sodium acetate pH 4.8, 2 M Ammoniumsulphate PH range: 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 64865 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.3 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4OQV Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.863 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.056 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.525 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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