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- PDB-6vty: Crystal structure of Plasmodium falciparum dihydroorotate dehydro... -

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Basic information

Entry
Database: PDB / ID: 6vty
TitleCrystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM483
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / mitochondria / alpha-beta barrel
Function / homology
Function and homology information


Pyrimidine biosynthesis / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane
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 class I / Aldolase-type TIM barrel / TIM Barrel ...Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / OROTIC ACID / Chem-RLA / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsDeng, X. / Phillips, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)U01AI075594 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria.
Authors: Kokkonda, S. / Deng, X. / White, K.L. / El Mazouni, F. / White, J. / Shackleford, D.M. / Katneni, K. / Chiu, F.C.K. / Barker, H. / McLaren, J. / Crighton, E. / Chen, G. / Angulo-Barturen, I. ...Authors: Kokkonda, S. / Deng, X. / White, K.L. / El Mazouni, F. / White, J. / Shackleford, D.M. / Katneni, K. / Chiu, F.C.K. / Barker, H. / McLaren, J. / Crighton, E. / Chen, G. / Angulo-Barturen, I. / Jimenez-Diaz, M.B. / Ferrer, S. / Huertas-Valentin, L. / Martinez-Martinez, M.S. / Lafuente-Monasterio, M.J. / Chittimalla, R. / Shahi, S.P. / Wittlin, S. / Waterson, D. / Burrows, J.N. / Matthews, D. / Tomchick, D. / Rathod, P.K. / Palmer, M.J. / Charman, S.A. / Phillips, M.A.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)199,53816
Polymers195,7874
Non-polymers3,75112
Water16,159897
1
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8854
Polymers48,9471
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8854
Polymers48,9471
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8854
Polymers48,9471
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8854
Polymers48,9471
Non-polymers9383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.088, 97.521, 186.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 48946.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFF0160c / Plasmid: pET28b / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q08210, dihydroorotate dehydrogenase (quinone)
#2: Chemical
ChemComp-RLA / ethyl 3,5-dimethyl-4-{[4-(trifluoromethyl)phenyl]methyl}-1H-pyrrole-2-carboxylate


Mass: 325.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18F3NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.17 M Ammonium Acetate, 0.1 M tri-Sodium citrate, pH 5.6, 25% PEG4000, 16% Glycerol 10 mM DTT
PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.78→42.03 Å / Num. obs: 161464 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 19 Å2 / Rpim(I) all: 0.03 / Net I/σ(I): 26.2
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8016 / CC1/2: 0.55 / Rpim(I) all: 0.656 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXV1.16refinement
HKL-2000V718data reduction
HKL-2000V718data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I65

3i65


Resolution: 1.78→42.03 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1939 --
Rwork0.1514 --
obs-148953 92.2 %
Displacement parametersBiso mean: 29.08 Å2
Refinement stepCycle: LAST / Resolution: 1.78→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11749 0 260 897 12906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019212300
X-RAY DIFFRACTIONf_angle_d1.511116609
X-RAY DIFFRACTIONf_chiral_restr0.08521837
X-RAY DIFFRACTIONf_plane_restr0.01252103
X-RAY DIFFRACTIONf_dihedral_angle_d15.7077434

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