+Open data
-Basic information
Entry | Database: PDB / ID: 7orc | ||||||
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Title | Human Aldehyde Oxidase in complex with Raloxifene | ||||||
Components | Aldehyde oxidase | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Mota, C. / Coelho, C. / Santos Silva, T. / Romao, M.J. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7orc.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7orc.ent.gz | 839.7 KB | Display | PDB format |
PDBx/mmJSON format | 7orc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7orc_validation.pdf.gz | 777.1 KB | Display | wwPDB validaton report |
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Full document | 7orc_full_validation.pdf.gz | 799.2 KB | Display | |
Data in XML | 7orc_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 7orc_validation.cif.gz | 75.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/7orc ftp://data.pdbj.org/pub/pdb/validation_reports/or/7orc | HTTPS FTP |
-Related structure data
Related structure data | 7opnC 4uhwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | 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 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MLI / #7: Chemical | ChemComp-RAL / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG3350, Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.7→2.75 Å / Num. unique obs: 4528 / CC1/2: 0.611 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 4 - 1336
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