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- PDB-9m2a: The crystal structure of the trypanosome alternative oxidase comp... -

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Basic information

Entry
Database: PDB / ID: 9m2a
TitleThe crystal structure of the trypanosome alternative oxidase complexed with a trypanocidal phosphonium derivative (compound1)
ComponentsAlternative oxidase, mitochondrial
KeywordsOXIDOREDUCTASE / ALTERNATIVE OXIDASE / INHIBITOR / DRUG / AFRICAN TRYPANOSOMES
Function / homology
Function and homology information


alternative oxidase activity / alternative respiration / Oxidoreductases / ferric iron binding / oxidoreductase activity / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Alternative oxidase / Alternative oxidase superfamily / Alternative oxidase
Similarity search - Domain/homology
: / : / HYDROXIDE ION / Alternative oxidase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsEbiloma, G.U. / Balogun, E.O. / Dardonville, C. / De Koning, H.P. / Shiba, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Uncovering the Unusual Inhibition Mechanism of a Trypanosome Alternative Oxidase Inhibitor Displaying Broad-Spectrum Activity against African Animal Trypanosomes.
Authors: Ebiloma, G.U. / Balogun, E.O. / Arai, N. / Otani, M. / Baldassarri, C. / Alhejely, A. / Cueto-Diaz, E. / De Koning, H.P. / Dardonville, C. / Shiba, T.
History
DepositionFeb 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alternative oxidase, mitochondrial
B: Alternative oxidase, mitochondrial
C: Alternative oxidase, mitochondrial
D: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,61617
Polymers125,4894
Non-polymers1,12713
Water00
1
A: Alternative oxidase, mitochondrial
B: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6149
Polymers62,7452
Non-polymers8697
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-132 kcal/mol
Surface area23220 Å2
MethodPISA
2
C: Alternative oxidase, mitochondrial
D: Alternative oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0028
Polymers62,7452
Non-polymers2576
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-134 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.368, 221.727, 62.855
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Alternative oxidase, mitochondrial


Mass: 31372.283 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: AOX / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q26710, Oxidoreductases
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1L8E / 14-[diphenyl(pyridin-2-yl)-$l^{5}-phosphanyl]tetradecyl 2-methyl-4-oxidanyl-benzoate


Mass: 611.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H50NO3P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 30% PEG 400, 0.1 M IMIDAZOLE, 0.5M POTASSIUM FORMATE, PH 7.4
PH range: 7.0-7.5

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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 PILATUS 2M / Detector: PIXEL / Date: Dec 25, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.01→50 Å / Num. obs: 35302 / % possible obs: 92 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.3
Reflection shellResolution: 3.01→3.05 Å / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1498 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVA

3vva


Resolution: 3.01→44.96 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.859 / SU B: 5.606 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25353 1491 4.9 %RANDOM
Rwork0.19452 ---
obs0.1975 28877 81.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.58 Å2
2---0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 3.01→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8749 0 56 0 8805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198996
X-RAY DIFFRACTIONr_bond_other_d0.0040.028778
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.95912217
X-RAY DIFFRACTIONr_angle_other_deg1.1743.00220065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.51451074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91122.212416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.351151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7081596
X-RAY DIFFRACTIONr_chiral_restr0.0930.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219958
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022178
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8486.6994308
X-RAY DIFFRACTIONr_mcbond_other3.8486.6994307
X-RAY DIFFRACTIONr_mcangle_it6.24810.0365378
X-RAY DIFFRACTIONr_mcangle_other6.24810.0375379
X-RAY DIFFRACTIONr_scbond_it3.2316.9174685
X-RAY DIFFRACTIONr_scbond_other3.236.9184686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.38510.36839
X-RAY DIFFRACTIONr_long_range_B_refined9.38153.60410935
X-RAY DIFFRACTIONr_long_range_B_other9.38153.60810936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.01→3.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.138 19 -
Rwork0.194 780 -
obs--29.69 %

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