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- PDB-7orc: Human Aldehyde Oxidase in complex with Raloxifene -

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Basic information

Entry
Database: PDB / ID: 7orc
TitleHuman Aldehyde Oxidase in complex with Raloxifene
ComponentsAldehyde oxidase
KeywordsOXIDOREDUCTASE / Human Aldehyde Oxidase / 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 / 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. / 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. / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / 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 / RALOXIFENE / Aldehyde oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 5, 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)301,88320
Polymers296,1932
Non-polymers5,69018
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14580 Å2
ΔGint-116 kcal/mol
Surface area90420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.033, 149.033, 268.734
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: 148096.500 Da / Num. of mol.: 2
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 , 7 types, 193 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) 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


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


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical
ChemComp-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H27NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
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: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→49.05 Å / Num. obs: 83694 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 50.55 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.9
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 4528 / CC1/2: 0.611

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UHW

4uhw


Resolution: 2.7→48.85 Å / SU ML: 0.3375 / Cross valid method: FREE R-VALUE / σ(F): 0.95 / Phase error: 28.4585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2521 4163 4.98 %
Rwork0.2186 79381 -
obs0.2203 83544 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.94 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20139 0 342 175 20656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002120934
X-RAY DIFFRACTIONf_angle_d0.522728334
X-RAY DIFFRACTIONf_chiral_restr0.04123131
X-RAY DIFFRACTIONf_plane_restr0.00413640
X-RAY DIFFRACTIONf_dihedral_angle_d15.96167977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.34441310.34152635X-RAY DIFFRACTION100
2.73-2.760.34611630.33872558X-RAY DIFFRACTION100
2.76-2.80.37121550.32192590X-RAY DIFFRACTION100
2.8-2.830.37561430.31252579X-RAY DIFFRACTION100
2.83-2.870.34141380.31052643X-RAY DIFFRACTION100
2.87-2.910.3141200.29992596X-RAY DIFFRACTION100
2.91-2.950.33321430.29272615X-RAY DIFFRACTION100
2.95-2.990.31211330.28292622X-RAY DIFFRACTION100
2.99-3.040.28651430.28412631X-RAY DIFFRACTION99.96
3.04-3.090.31951280.27912581X-RAY DIFFRACTION99.93
3.09-3.140.30671290.26652659X-RAY DIFFRACTION100
3.14-3.20.29261360.27782612X-RAY DIFFRACTION99.96
3.2-3.260.3231590.25982588X-RAY DIFFRACTION100
3.26-3.330.28321250.26292651X-RAY DIFFRACTION100
3.33-3.40.29911480.24292635X-RAY DIFFRACTION99.96
3.4-3.480.27641350.2382581X-RAY DIFFRACTION100
3.48-3.570.30931360.23092671X-RAY DIFFRACTION100
3.57-3.660.26781280.22672629X-RAY DIFFRACTION99.96
3.66-3.770.27191290.21482619X-RAY DIFFRACTION99.89
3.77-3.890.26951380.2162667X-RAY DIFFRACTION99.93
3.89-4.030.24281400.20182636X-RAY DIFFRACTION100
4.03-4.190.21281380.18632649X-RAY DIFFRACTION100
4.19-4.380.21131470.18152680X-RAY DIFFRACTION99.96
4.38-4.620.21841290.17812648X-RAY DIFFRACTION99.96
4.62-4.90.17681410.16682667X-RAY DIFFRACTION99.93
4.9-5.280.20411310.17562709X-RAY DIFFRACTION99.96
5.28-5.810.19461420.19012674X-RAY DIFFRACTION99.96
5.81-6.650.25371530.20282710X-RAY DIFFRACTION99.97
6.65-8.380.22071300.17142782X-RAY DIFFRACTION100
8.38-48.850.16031520.16182864X-RAY DIFFRACTION98.5
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.434282558006-0.189612010408-0.1718574486890.6539737735360.5873820368890.8034812652690.02991677930150.1126069241450.0192686315172-0.0506109712067-0.0250575152477-0.07913703552980.04256497027740.0398629956107-0.001396475512540.4776782038070.04234948032450.03374675338260.2930522930850.02679916299990.354173962308-21.7129165315-46.528686873440.2040467878
20.660958309876-0.0739723699969-0.2423777490290.6200312630290.2897832014540.848535027286-0.0767301714781-0.1706951044240.03968152099190.1439311207070.0335363423554-0.01812213073230.0623907834697-0.02332577639830.03829609879810.447093253045-0.0061313968546-0.01836579395270.25019824101-0.05254310722430.35140528685-46.5460419861-21.721085540196.8396445288
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11(chain 'A' and resid 4 through 1336)AA1 - 1295
22(chain 'B' and resid 4 through 1336)BB1 - 1299

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