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Open data
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Basic information
Entry | Database: PDB / ID: 2ckj | ||||||
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Title | Human milk xanthine oxidoreductase | ||||||
![]() | XANTHINE OXIDOREDUCTASE | ||||||
![]() | OXIDOREDUCTASE / FAD / NAD / IRON / 2FE-2S / MOLYBDENUM / PEROXISOME / REVERSIBLE INTERCONVERSION / XANTHINE DEHYDROGENASE / XANTHINE OXIDOREDUCTASE / XANTHINE OXIDASE / IRON-SULFUR / POLYMORPHISM / FLAVOPROTEIN / METAL-BINDING | ||||||
Function / homology | ![]() hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / negative regulation of endothelial cell differentiation / xanthine dehydrogenase / xanthine oxidase ...hypoxanthine catabolic process / hypoxanthine dehydrogenase activity / hypoxanthine oxidase activity / negative regulation of vasculogenesis / guanine catabolic process / deoxyguanosine catabolic process / dGMP catabolic process / negative regulation of endothelial cell differentiation / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / GMP catabolic process / xanthine dehydrogenase activity / Butyrophilin (BTN) family interactions / amide catabolic process / deoxyinosine catabolic process / adenosine catabolic process / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / negative regulation of vascular endothelial growth factor signaling pathway / AMP catabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / molybdopterin cofactor binding / Azathioprine ADME / positive regulation of p38MAPK cascade / iron-sulfur cluster assembly / negative regulation of endothelial cell proliferation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lactation / FAD binding / negative regulation of protein phosphorylation / sarcoplasmic reticulum / 2 iron, 2 sulfur cluster binding / peroxisome / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of reactive oxygen species metabolic process / flavin adenine dinucleotide binding / iron ion binding / negative regulation of gene expression / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pearson, A.R. / Godber, B.L.J. / Eisenthal, R. / Taylor, G.L. / Harrison, R. | ||||||
![]() | ![]() Title: Human Milk Xanthine Dehydrogenase is Incompletely Converted to the Oxidase Form in the Absence of Proteolysis. A Structural Explanation. Authors: Pearson, A.R. / Godber, B.L.J. / Eisenthal, R. / Taylor, G.L. / Harrison, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1007.1 KB | Display | ![]() |
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PDB format | ![]() | 796.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.3 KB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 166.5 KB | Display | |
Data in CIF | ![]() | 224.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fo4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 146601.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: MILK KINDLY DONATED BY MOTHERS AT THE INTENSIVE CARE BABY UNITS AT THE BRISTOL ROYAL INFIRMARY AND SOUTHMEAD HOSPITAL, BRISTOL, UK Source: (natural) ![]() References: UniProt: P47989, 1.1.1.204, EC: 1.2.3.2, xanthine oxidase |
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-Non-polymers , 5 types, 18 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PO4.gif)
#2: Chemical | ChemComp-FES / #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACY / | #6: Chemical | ChemComp-PO4 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | pH: 6 Details: 26% (W/V) PEG 4K, 0.1M SODIUM ACETATE, PH 6, 0.25M AMMONIUM ACETATE, 10MM DTT, 10% (W/V) GLUCOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 75088 / % possible obs: 98.2 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 3.5→3.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.5 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FO4 Resolution: 3.59→30.76 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.841 / SU B: 68.993 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.71 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-2, A166-192, A426-429, A534-557, A1231-A1328, A1330-1333, B1, B166-192, B548-556, B1320-1325, B1333, C1-2, C166-192, C429-431, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-2, A166-192, A426-429, A534-557, A1231-A1328, A1330-1333, B1, B166-192, B548-556, B1320-1325, B1333, C1-2, C166-192, C429-431, C548-556, C1320-1327, C1333, D1-2, D166-192, D542-556, D1321-1325, D1333 ARE NOT PRESENT IN THE ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.75 Å2
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Refinement step | Cycle: LAST / Resolution: 3.59→30.76 Å
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Refine LS restraints |
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