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- PDB-6dpr: Mapping the binding trajectory of a suicide inhibitor in human in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dpr | |||||||||
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Title | Mapping the binding trajectory of a suicide inhibitor in human indoleamine 2,3-dioxygenase 1 | |||||||||
![]() | Indoleamine 2,3-dioxygenase 1 | |||||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / indoleamine 2 / 3-dioxygenase / heme-containing enzyme / BMS-986205 / structure-based design / hIDO1-selective inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Pham, K.N. / Yeh, S.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mapping the Binding Trajectory of a Suicide Inhibitor in Human Indoleamine 2,3-Dioxygenase 1. Authors: Pham, K.N. / 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 | ![]() | 166.2 KB | Display | ![]() |
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PDB format | ![]() | 128.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dpqC ![]() 6mq6C ![]() 5wmuS 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: 47704.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 10 Details: 100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 200 mM sodium chloride, 20% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 17, 2017 |
Radiation | Monochromator: double crystal diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→29.5 Å / Num. obs: 18253 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.101 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.465 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1612 / CC1/2: 0.508 / Rpim(I) all: 0.588 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5WMU Resolution: 3.2→29.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 27.048 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / 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: 85.609 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→29.5 Å
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Refine LS restraints |
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