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- PDB-5d96: Oxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Frag... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d96 | ||||||
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Title | Oxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Fragment from an Antibody Targeting Mouse and Human QSOX1 | ||||||
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![]() | IMMUNE SYSTEM / enzyme / inhibitor / antibody / dual-specificity | ||||||
Function / homology | ![]() flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation / FAD binding / protein folding / Golgi membrane / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fass, D. / Grossman, I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Overcoming a species-specificity barrier in development of an inhibitory antibody targeting a modulator of tumor stroma. Authors: Grossman, I. / Ilani, T. / Fleishman, S.J. / Fass, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 270.6 KB | Display | ![]() |
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PDB format | ![]() | 215.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.9 KB | Display | ![]() |
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Full document | ![]() | 475.1 KB | Display | |
Data in XML | ![]() | 50 KB | Display | |
Data in CIF | ![]() | 71.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d8iSC ![]() 5d93C ![]() 4ij3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27005.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 23551.092 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 23452.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM CaCl2, 0.1 M 2-(N-morpholino)ethanesulfonic acid buffer, pH 6, 22.5% w/v PEG 6 kD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 62461 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D8I, 4IJ3 Resolution: 2.3→27.424 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.26 / Stereochemistry target values: TWIN_LSQ_F
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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: 34.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→27.424 Å
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Refine LS restraints |
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LS refinement shell |
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