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Yorodumi- PDB-5wmx: Structural Insights into Substrate and Inhibitor Binding Sites in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wmx | ||||||||||||
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Title | Structural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1 | ||||||||||||
Components | Indoleamine 2,3-dioxygenase 1 | ||||||||||||
Keywords | OXIDOREDUCTASE / Dioxygenase Tryptophan Heme Inhibitor | ||||||||||||
Function / homology | Function and homology information 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 / positive regulation of T cell apoptotic process / negative 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||||||||
Authors | Lewis-Ballester, A. / Yeh, S.R. / Pham, K.N. / Batabyal, D. / Karkashon, S. / Bonanno, J.B. / Poulos, T.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wmx.cif.gz | 326.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wmx.ent.gz | 268.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/5wmx ftp://data.pdbj.org/pub/pdb/validation_reports/wm/5wmx | HTTPS FTP |
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-Related structure data
Related structure data | 5wmuC 5wmvC 5wmwC 5wn8C 2d0tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47701.797 Da / Num. of mol.: 2 / Mutation: F270G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli (E. coli) / References: UniProt: P14902, indoleamine 2,3-dioxygenase |
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-Non-polymers , 5 types, 139 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.68 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 10 Details: 100 mM Sodium thiosulfate, 100 mM pH 10.0 CAPS buffer, and 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016 / Details: mirror |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→39.1 Å / Num. obs: 31517 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.033 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.69→2.76 Å / Redundancy: 6 % / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4082 / CC1/2: 0.44 / Rpim(I) all: 0.85 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D0T Resolution: 2.69→39.1 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 36.34 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.719 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.372 Å2
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Refinement step | Cycle: 1 / Resolution: 2.69→39.1 Å
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