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Yorodumi- PDB-3zws: Structure of Human Dihydroorotate Dehydrogenase with a Bound Inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zws | ||||||
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Title | Structure of Human Dihydroorotate Dehydrogenase with a Bound Inhibitor | ||||||
Components | DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIALDihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 / OTHER / Resolution: 1.6 Å | ||||||
Authors | Acklam, P.A. / Parsons, M.R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Factors Influencing the Specificity of Inhibitor Binding to the Human and Malaria Parasite Dihydroorotate Dehydrogenases. Authors: Bedingfield, P.T.P. / Cowen, D. / Acklam, P.A. / Cunningham, F. / Parsons, M.R. / Mcconkey, G.A. / Fishwick, C.W.G. / Johnson, A.P. | ||||||
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 | 3zws.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zws.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/3zws ftp://data.pdbj.org/pub/pdb/validation_reports/zw/3zws | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39856.535 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone), EC: 1.3.3.1 |
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-Non-polymers , 7 types, 263 molecules
#2: Chemical | ChemComp-FMN / | ||||||||
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#3: Chemical | ChemComp-ORO / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-AVQ / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-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 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM ACETATE (PH 4.8), 2.4-2.6 M AMMONIUM SULPHATE, 40 MM C11DAO, 20 MM DDAO. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.42 Å / Num. obs: 77716 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 15.213 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.6→37.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.962 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→37.42 Å
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