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- PDB-8yhr: DHODH in complex with furocoumavirin -

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Basic information

Entry
Database: PDB / ID: 8yhr
TitleDHODH in complex with furocoumavirin
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / dihydroorotate dehydrogenase / dhodh / inhibitor
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / 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) / dihydroorotate dehydrogenase (quinone) activity / 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
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / ACETATE ION / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHara, K. / Okumura, H. / Nakahara, M. / Sato, M. / Hashimoto, H. / Osada, H. / Watanabe, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2024
Title: Structural and Functional Analyses of Inhibition of Human Dihydroorotate Dehydrogenase by Antiviral Furocoumavirin.
Authors: Nakahara, M. / Watanabe, S. / Sato, M. / Okumura, H. / Kawatani, M. / Osada, H. / Hara, K. / Hashimoto, H. / Watanabe, K.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,69013
Polymers42,0281
Non-polymers1,66212
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.627, 90.627, 122.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydroorotate dehydrogenase (quinone), mitochondrial / DHOdehase / Dihydroorotate oxidase


Mass: 42027.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli)
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 7 types, 282 molecules

#2: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-A1LYU / 4-methyl-8-[(S)-oxidanyl(phenyl)methyl]-9-phenyl-furo[2,3-h]chromen-2-one


Mass: 382.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H18O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Sodium acetate (pH 4.8), Ammonium sulfate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→36.4 Å / Num. obs: 63419 / % possible obs: 98.57 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0729 / Net I/σ(I): 17.99
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 5673 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.395 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1645 1990 3.14 %
Rwork0.1459 --
obs0.1465 63410 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 114 270 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092855
X-RAY DIFFRACTIONf_angle_d1.2483856
X-RAY DIFFRACTIONf_dihedral_angle_d13.8681059
X-RAY DIFFRACTIONf_chiral_restr0.049424
X-RAY DIFFRACTIONf_plane_restr0.008502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.20281300.19033871X-RAY DIFFRACTION88
1.7425-1.78970.18731360.16734132X-RAY DIFFRACTION94
1.7897-1.84230.18391390.15774301X-RAY DIFFRACTION98
1.8423-1.90180.18211430.14754392X-RAY DIFFRACTION100
1.9018-1.96970.1481440.13784429X-RAY DIFFRACTION100
1.9697-2.04860.16231430.13364385X-RAY DIFFRACTION100
2.0486-2.14180.15271450.13714430X-RAY DIFFRACTION100
2.1418-2.25470.17161420.13384419X-RAY DIFFRACTION100
2.2547-2.3960.15481460.13344436X-RAY DIFFRACTION100
2.396-2.58090.16381390.13914464X-RAY DIFFRACTION100
2.5809-2.84060.16211400.14014466X-RAY DIFFRACTION100
2.8406-3.25140.16081440.14464466X-RAY DIFFRACTION100
3.2514-4.09550.14991470.14064536X-RAY DIFFRACTION100
4.0955-36.3950.17671520.16224693X-RAY DIFFRACTION100

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