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- PDB-4uhx: Human aldehyde oxidase in complex with phthalazine and thioridazine -

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Basic information

Entry
Database: PDB / ID: 4uhx
TitleHuman aldehyde oxidase in complex with phthalazine and thioridazine
ComponentsALDEHYDE OXIDASE
KeywordsOXIDOREDUCTASE / ALDEHYDE OXIDASE / DRUG METABOLISM / MOLYBDENUM ENZYMES / XANTHINE OXIDASE / PHTHALAZINE / THIORIDAZINE
Function / homology
Function and homology information


Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / xenobiotic metabolic process / FAD binding / lipid metabolic process / 2 iron, 2 sulfur cluster binding / NAD binding ...Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / xenobiotic metabolic process / FAD binding / lipid metabolic process / 2 iron, 2 sulfur cluster binding / NAD binding / flavin adenine dinucleotide binding / iron ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Aldehyde oxidase / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding ...Aldehyde oxidase / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / FAD-binding, type PCMH, subdomain 1 / Aldehyde Oxidoreductase; domain 3 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / Enolase-like; domain 1 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
phthalazine / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-LZU / MALONATE ION / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / Chem-RTZ / Aldehyde oxidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCoelho, C. / Romao, M.J. / Santos-Silva, T.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Structural Insights Into Xenobiotic and Inhibitor Binding to Human Aldehyde Oxidase
Authors: Coelho, C. / Foti, A. / Hartmann, T. / Santos-Silva, T. / Leimkuhler, S. / Romao, M.J.
History
DepositionMar 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDEHYDE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,86511
Polymers148,0971
Non-polymers2,76910
Water1,08160
1
A: ALDEHYDE OXIDASE
hetero molecules

A: ALDEHYDE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,73122
Polymers296,1932
Non-polymers5,53820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area12620 Å2
ΔGint-107.9 kcal/mol
Surface area88840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.732, 148.732, 132.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ALDEHYDE OXIDASE / / ALDEHYDE OXIDASE 1 / AZAHETEROCYCLE HYDROXYLASE


Mass: 148096.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: Q06278, aldehyde oxidase

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Non-polymers , 9 types, 70 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#4: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2S
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-4FT / phthalazine / Phthalazine


Mass: 130.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6N2
#7: Chemical ChemComp-LZU / 10-{2-[(2S)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine / Thioridazine / Thioridazine


Mass: 370.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N2S2 / Comment: antipsychotic*YM
#8: Chemical ChemComp-RTZ / 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine


Mass: 370.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N2S2
#9: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.77 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→74.4 Å / Num. obs: 41407 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.2
Reflection shellResolution: 2.7→2.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZYV

3zyv


Resolution: 2.7→105.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 32.29 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24408 2085 5 %RANDOM
Rwork0.19526 ---
obs0.19774 39322 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.7→105.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10000 0 163 60 10223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910384
X-RAY DIFFRACTIONr_bond_other_d0.0020.029999
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.98614049
X-RAY DIFFRACTIONr_angle_other_deg0.9443.00223069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85851284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3124.182428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.343151802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3021556
X-RAY DIFFRACTIONr_chiral_restr0.0650.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022295
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_it0.9335.2395154
X-RAY DIFFRACTIONr_mcbond_other0.9335.2395153
X-RAY DIFFRACTIONr_mcangle_it1.6647.8546432
X-RAY DIFFRACTIONr_mcangle_other1.6647.8546433
X-RAY DIFFRACTIONr_scbond_it0.7935.4395230
X-RAY DIFFRACTIONr_scbond_other0.7925.4385228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3898.1117613
X-RAY DIFFRACTIONr_long_range_B_refined3.29941.69311115
X-RAY DIFFRACTIONr_long_range_B_other3.29941.69111112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 142 -
Rwork0.357 2835 -
obs--98.25 %
Refinement TLS params.Method: refined / Origin x: -46.626 Å / Origin y: -21.422 Å / Origin z: -38.334 Å
111213212223313233
T0.1662 Å20.04 Å20.0044 Å2-0.1871 Å2-0.1192 Å2--0.084 Å2
L0.951 °2-0.1108 °2-0.4526 °2-0.7318 °20.195 °2--0.861 °2
S-0.0507 Å °-0.2501 Å °0.1537 Å °0.2464 Å °-0.011 Å °0.0744 Å °-0.0418 Å °-0.0535 Å °0.0617 Å °

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