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- PDB-7z2l: Crystal structure of L-Kynurenine in the active site of human Ind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z2l | ||||||
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Title | Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1) | ||||||
![]() | Indoleamine 2,3-dioxygenase 1![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mirgaux, M. / Wouters, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1) Authors: Mirgaux, M. / Wouters, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 406.2 KB | Display | ![]() |
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PDB format | ![]() | 267.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ngeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | ![]() Mass: 45300.898 Da / Num. of mol.: 4 / Mutation: K116A, K117A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 929 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KYN.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KYN.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / ![]() #3: Chemical | ChemComp-GOL / ![]() #4: Chemical | ChemComp-KYN / ( ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % / Description: Red rectangular crystal |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Well : 0.1M Phosphate buffer, pH= 6.2, PEG 3350 = 16% Protein: 5mM Hepes, 200mM NaCl, 5mM DTT Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2021 / Details: channel-cut |
Radiation | Monochromator: channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.56→47.23 Å / Num. obs: 66614 / % possible obs: 99.18 % / Redundancy: 13.6 % / Biso Wilson estimate: 42.15 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.09638 / Net I/σ(I): 13.33 |
Reflection shell | Resolution: 2.562→2.654 Å / Mean I/σ(I) obs: 2.22 / Num. unique obs: 6308 / CC1/2: 0.855 / CC star: 0.96 / Rpim(I) all: 0.5299 / % possible all: 93.96 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7NGE Resolution: 2.56→47.23 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4074 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: 46.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→47.23 Å
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Refine LS restraints |
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LS refinement shell |
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