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Yorodumi- PDB-2wv8: Complex of human dihydroorotate dehydrogenase with the inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wv8 | ||||||
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Title | Complex of human dihydroorotate dehydrogenase with the inhibitor 221290 | ||||||
Components | DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / TRANSMEMBRANE / MITOCHONDRION INNER MEMBRANE / TRANSIT PEPTIDE / ENZYME INHIBITION / PYRIMIDINE BIOSYNTHESIS / STRUCTURE-BASED DRUG DESIGN / INFLAMATION | ||||||
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: 1.9 Å | ||||||
Authors | Walse, B. / Svensson, B. / Fritzson, I. / Dahlberg, L. / Wellmar, U. / Al-Karadaghi, S. | ||||||
Citation | Journal: Chemmedchem / Year: 2010 Title: Inhibition of Human Dhodh by 4-Hydroxycoumarins, Fenamic Acids, and N-(Alkylcarbonyl)Anthranilic Acids Identified by Structure-Guided Fragment Selection. Authors: Fritzson, I. / Svensson, B. / Al-Karadaghi, S. / Walse, B. / Wellmar, U. / Nilsson, U.J. / Da Graca Thrige, D. / Jonsson, 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 | 2wv8.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wv8.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 2wv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wv8 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wv8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39654.266 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 7 types, 354 molecules
#2: Chemical | ChemComp-FMN / |
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#3: Chemical | ChemComp-ORO / |
#4: Chemical | ChemComp-VGN / |
#5: Chemical | ChemComp-DDQ / |
#6: Chemical | ChemComp-ACT / |
#7: Chemical | ChemComp-SO4 / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.57 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Type: MAX II / Wavelength: 1.017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.017 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 44920 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.38 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2791550.09 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.7489 Å2 / ksol: 0.401457 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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