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- PDB-5x68: Crystal Structure of Human KMO -

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Basic information

Entry
Database: PDB / ID: 5x68
TitleCrystal Structure of Human KMO
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / monooxygenase / flavin reduction
Function / homology
Function and homology information


L-kynurenine metabolic process / positive regulation of glutamate secretion, neurotransmission / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / anthranilate metabolic process / kynurenic acid biosynthetic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / NAD(P)H oxidase H2O2-forming activity / quinolinate biosynthetic process ...L-kynurenine metabolic process / positive regulation of glutamate secretion, neurotransmission / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / anthranilate metabolic process / kynurenic acid biosynthetic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / NAD(P)H oxidase H2O2-forming activity / quinolinate biosynthetic process / L-tryptophan catabolic process / Tryptophan catabolism / NAD+ metabolic process / cellular response to interleukin-1 / response to salt stress / FAD binding / flavin adenine dinucleotide binding / cellular response to lipopolysaccharide / mitochondrial outer membrane / extracellular space / cytosol
Similarity search - Function
Kynurenine 3-monooxygenase / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKim, H.T. / Hwang, K.Y.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase
Authors: Kim, H.T. / Na, B.K. / Chung, J. / Kim, S. / Kwon, S.K. / Cha, H. / Son, J. / Cho, J.M. / Hwang, K.Y.
History
DepositionFeb 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kynurenine 3-monooxygenase
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1414
Polymers88,5702
Non-polymers1,5712
Water2,360131
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0712
Polymers44,2851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area17510 Å2
MethodPISA
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0712
Polymers44,2851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-6 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.736, 176.736, 89.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Kynurenine 3-monooxygenase / Kynurenine 3-hydroxylase


Mass: 44285.121 Da / Num. of mol.: 2 / Fragment: UNP residues 1-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMO / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O15229, kynurenine 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris (pH 8.5), 13% polyethylene glycol 4000, and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: AREA DETECTOR / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→88.37 Å / Num. obs: 55790 / % possible obs: 96.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Rsym value: 0.063 / Net I/σ(I): 25.6
Reflection shellRedundancy: 2.4 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.315

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→88.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.433 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2972 5.1 %RANDOM
Rwork0.209 ---
obs0.211 55790 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→88.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 106 131 5859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0195927
X-RAY DIFFRACTIONr_bond_other_d00.025646
X-RAY DIFFRACTIONr_angle_refined_deg0.6661.9768033
X-RAY DIFFRACTIONr_angle_other_deg0.498313030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13323.885260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2921533
X-RAY DIFFRACTIONr_chiral_restr0.0450.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0216887
X-RAY DIFFRACTIONr_gen_planes_other00.021354
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_it2.8315.2852846
X-RAY DIFFRACTIONr_mcbond_other2.8295.2842845
X-RAY DIFFRACTIONr_mcangle_it4.3297.9133554
X-RAY DIFFRACTIONr_mcangle_other4.3297.9143555
X-RAY DIFFRACTIONr_scbond_it3.2275.6613081
X-RAY DIFFRACTIONr_scbond_other3.2275.6643078
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1738.3264473
X-RAY DIFFRACTIONr_long_range_B_refined7.50542.2186557
X-RAY DIFFRACTIONr_long_range_B_other7.49242.216546
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 189 -
Rwork0.376 3839 -
obs--88.61 %

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