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- PDB-7opn: Human Aldehyde Oxidase SNP R1231H in complex with Raloxifene -

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Basic information

Entry
Database: PDB / ID: 7opn
TitleHuman Aldehyde Oxidase SNP R1231H in complex with Raloxifene
ComponentsAldehyde oxidase
KeywordsOXIDOREDUCTASE / Human Aldehyde Oxidase / Single Nucleotide Polymorphism / Complex / Inhibitor
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 / 2 iron, 2 sulfur cluster binding / lipid metabolic process / 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 / 2 iron, 2 sulfur cluster binding / lipid metabolic process / 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. / CO dehydrogenase flavoprotein C-terminal 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 / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal 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 / FAD-binding, type PCMH, subdomain 1 / 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 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / MALONATE ION / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / Chem-PG6 / RALOXIFENE / Aldehyde oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMota, C. / Coelho, C. / Santos Silva, T. / Romao, M.J.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/1185/2014 Portugal
CitationJournal: J.Med.Chem. / Year: 2021
Title: Interrogating the Inhibition Mechanisms of Human Aldehyde Oxidase by X-ray Crystallography and NMR Spectroscopy: The Raloxifene Case.
Authors: Mota, C. / Diniz, A. / Coelho, C. / Santos-Silva, T. / Esmaeeli, M. / Leimkuhler, S. / Cabrita, E.J. / Marcelo, F. / Romao, M.J.
History
DepositionJun 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde oxidase
B: Aldehyde oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,26123
Polymers296,1552
Non-polymers6,10621
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16210 Å2
ΔGint-100 kcal/mol
Surface area89900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.528, 149.528, 269.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde oxidase / / Aldehyde oxidase 1 / Azaheterocycle hydroxylase


Mass: 148077.453 Da / Num. of mol.: 2 / Mutation: R1231H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AOX1, AO / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MC4100 / Variant (production host): TP1000
References: UniProt: Q06278, aldehyde oxidase, Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor

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Non-polymers , 10 types, 184 molecules

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


Mass: 175.820 Da / Num. of mol.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#4: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMoO2S
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-RAL / RALOXIFENE / Raloxifene


Mass: 473.583 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H27NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#10: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG3350, Sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.6→49.01 Å / Num. obs: 94428 / % possible obs: 100 % / Redundancy: 15.4 % / Biso Wilson estimate: 55.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.1
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 4609 / CC1/2: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UHW
Resolution: 2.6→49.01 Å / SU ML: 0.3305 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 29.4604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 4727 5.02 %RANDOM
Rwork0.2059 89502 --
obs0.2076 94229 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20110 0 368 163 20641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002420938
X-RAY DIFFRACTIONf_angle_d0.551828331
X-RAY DIFFRACTIONf_chiral_restr0.04183129
X-RAY DIFFRACTIONf_plane_restr0.00443633
X-RAY DIFFRACTIONf_dihedral_angle_d16.03297970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.35851370.34652993X-RAY DIFFRACTION100
2.63-2.660.40161500.33452920X-RAY DIFFRACTION99.97
2.66-2.690.36331650.32222920X-RAY DIFFRACTION100
2.69-2.730.35091670.32392943X-RAY DIFFRACTION100
2.73-2.760.37911430.31562963X-RAY DIFFRACTION100
2.76-2.80.33331390.2932948X-RAY DIFFRACTION100
2.8-2.840.29531650.28722934X-RAY DIFFRACTION99.97
2.84-2.880.31451750.27922971X-RAY DIFFRACTION100
2.88-2.930.32541590.27652938X-RAY DIFFRACTION100
2.93-2.980.35161560.26972939X-RAY DIFFRACTION99.97
2.98-3.030.3171560.26522963X-RAY DIFFRACTION99.94
3.03-3.080.27021640.25892925X-RAY DIFFRACTION99.94
3.08-3.140.29831620.2622950X-RAY DIFFRACTION99.94
3.14-3.210.30341800.26632950X-RAY DIFFRACTION99.94
3.21-3.280.29631490.242972X-RAY DIFFRACTION100
3.28-3.350.26491650.24092946X-RAY DIFFRACTION100
3.35-3.440.25191580.21382948X-RAY DIFFRACTION99.94
3.44-3.530.24681680.21062979X-RAY DIFFRACTION100
3.53-3.630.24311490.21272983X-RAY DIFFRACTION99.9
3.63-3.750.21421600.1992965X-RAY DIFFRACTION99.97
3.75-3.880.25481500.19872970X-RAY DIFFRACTION100
3.88-4.040.2021490.17573009X-RAY DIFFRACTION99.84
4.04-4.220.18671680.16842997X-RAY DIFFRACTION99.97
4.22-4.440.20351680.16022981X-RAY DIFFRACTION99.97
4.45-4.720.19821590.15733005X-RAY DIFFRACTION99.94
4.72-5.090.19071670.16153033X-RAY DIFFRACTION99.94
5.09-5.60.22031550.17373042X-RAY DIFFRACTION99.97
5.6-6.410.24511530.18953082X-RAY DIFFRACTION100
6.41-8.070.20331320.17513124X-RAY DIFFRACTION99.97
8.07-49.010.16471590.15723209X-RAY DIFFRACTION97.57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.711459765864-0.127594562187-0.3748050937780.5762537795730.2566368241241.07636423589-0.0405462385198-0.1434011864940.0353839016550.1292156639740.0293972572134-0.03169716514210.013801890812-0.02448555330730.01958240187780.403493312490.0181739431266-0.02829141531020.283828173232-0.06054446085920.370133569489-46.7408411617-21.9269164355-37.6416425248
20.438686584969-0.122538725109-0.1816217766260.751038998070.5093304592020.9033791857330.02622978192490.117991549186-0.00317361277198-0.103882365108-0.0221069547702-0.09983266002240.07935756032710.0362453337398-0.00731941481970.4694553474570.04907812270430.04169536454270.3174458280440.0008250692252370.383836821107-21.8431814617-46.7913814347-94.4923097199
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 4 - 1336 / Label seq-ID: 1 - 1295

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 4 through 1336)AA
22(chain 'B' and resid 4 through 1336)BB

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