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- PDB-5wn8: Structural Insights into Substrate and Inhibitor Binding Sites in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wn8 | ||||||||||||
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Title | Structural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1 | ||||||||||||
![]() | Indoleamine 2,3-dioxygenase 1 | ||||||||||||
![]() | OXIDOREDUCTASE / Indoleamine 2 / 3-Dioxygenase 1 Tryptophan Heme Inhibitor Epacadostat INCB024360 | ||||||||||||
Function / homology | ![]() indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / T cell proliferation / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Lewis-Ballester, A. / Pham, K.N. / Batabyal, D. / Karkashon, S. / Bonanno, J.B. / Poulos, T.L. / Yeh, S.R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1. Authors: Lewis-Ballester, A. / Pham, K.N. / Batabyal, D. / Karkashon, S. / Bonanno, J.B. / Poulos, T.L. / Yeh, S.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 | ![]() | 167.8 KB | Display | ![]() |
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PDB format | ![]() | 130.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wmuC ![]() 5wmvC ![]() 5wmwC ![]() 5wmxC ![]() 2d0tS C: citing same article ( 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47791.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.1 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 9.5 Details: 100 mM Sodium thiosulfate, 100 mM CAPS buffer pH 9.5, and 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Mar 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91988 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.69 Å / Num. obs: 38582 / % possible obs: 99.9 % / Redundancy: 14.8 % / CC1/2: 0.59 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.023 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.5→2.565 Å / Redundancy: 14.9 % / Rmerge(I) obs: 2.3 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5556 / CC1/2: 0.59 / Rpim(I) all: 0.61 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2D0T Resolution: 2.5→29.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 11.624 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.263 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.291 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→29.69 Å
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Refine LS restraints |
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