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- PDB-6m2b: Crystal structure of human dihydroorotate dehydrogenase (DHODH) w... -

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Basic information

Entry
Database: PDB / ID: 6m2b
TitleCrystal structure of human dihydroorotate dehydrogenase (DHODH) with S416
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / inhibitor / complex / BIOSYNTHETIC PROTEIN
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
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
Chem-EZO / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZhu, L. / Li, H.
CitationJournal: Protein Cell / Year: 2020
Title: Novel and potent inhibitors targeting DHODH are broad-spectrum antivirals against RNA viruses including newly-emerged coronavirus SARS-CoV-2.
Authors: Xiong, R. / Zhang, L. / Li, S. / Sun, Y. / Ding, M. / Wang, Y. / Zhao, Y. / Wu, Y. / Shang, W. / Jiang, X. / Shan, J. / Shen, Z. / Tong, Y. / Xu, L. / Chen, Y. / Liu, Y. / Zou, G. / ...Authors: Xiong, R. / Zhang, L. / Li, S. / Sun, Y. / Ding, M. / Wang, Y. / Zhao, Y. / Wu, Y. / Shang, W. / Jiang, X. / Shan, J. / Shen, Z. / Tong, Y. / Xu, L. / Chen, Y. / Liu, Y. / Zou, G. / Lavillete, D. / Zhao, Z. / Wang, R. / Zhu, L. / Xiao, G. / Lan, K. / Li, H. / Xu, K.
History
DepositionFeb 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,6214
Polymers42,6361
Non-polymers9843
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.040, 91.040, 122.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 42636.414 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)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-EZO / 2-[(E)-[[4-(2-chlorophenyl)-1,3-thiazol-2-yl]-methyl-hydrazinylidene]methyl]benzoic acid


Mass: 371.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M acetate, 40mM UDAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97852 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.76→61.09 Å / Num. obs: 58612 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Net I/σ(I): 15
Reflection shellResolution: 1.76→1.86 Å / Num. unique obs: 8478 / CC1/2: 0.936

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LS1

4ls1


Resolution: 1.76→48.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.444 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2932 5 %RANDOM
Rwork0.1676 ---
obs0.1688 55638 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.64 Å2 / Biso mean: 19.346 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.76→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 67 145 3004
Biso mean--12.52 25.58 -
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132946
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172824
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.6744000
X-RAY DIFFRACTIONr_angle_other_deg1.4421.5936527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40920.382157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39515504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3711531
X-RAY DIFFRACTIONr_chiral_restr0.0880.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023347
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02630
LS refinement shellResolution: 1.76→1.806 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 211 -
Rwork0.191 4072 -
all-4283 -
obs--99.98 %

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