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- PDB-6v52: IDO1 IN COMPLEX WITH COMPOUND 1 -

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Basic information

Entry
Database: PDB / ID: 6v52
TitleIDO1 IN COMPLEX WITH COMPOUND 1
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / INDOLEAMINE DIOXYGENASE / 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 / 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
Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase signature 1. / Indoleamine 2,3-dioxygenase signature 2. / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
Chem-QPV / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsLesburg, C.A. / Koenig, K.V. / Augustin, M.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Strategic Incorporation of Polarity in Heme-Displacing Inhibitors of Indoleamine-2,3-dioxygenase-1 (IDO1).
Authors: White, C. / McGowan, M.A. / Zhou, H. / Sciammetta, N. / Fradera, X. / Lim, J. / Joshi, E.M. / Andrews, C. / Nickbarg, E.B. / Cowley, P. / Trewick, S. / Augustin, M. / von Koenig, K. / ...Authors: White, C. / McGowan, M.A. / Zhou, H. / Sciammetta, N. / Fradera, X. / Lim, J. / Joshi, E.M. / Andrews, C. / Nickbarg, E.B. / Cowley, P. / Trewick, S. / Augustin, M. / von Koenig, K. / Lesburg, C.A. / Otte, K. / Knemeyer, I. / Woo, H. / Yu, W. / Cheng, M. / Spacciapoli, P. / Geda, P. / Song, X. / Smotrov, N. / Curran, P. / Heo, M.R. / Abeywickrema, P. / Miller, J.R. / Bennett, D.J. / Han, Y.
History
DepositionDec 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Indoleamine 2,3-dioxygenase 1
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4524
Polymers88,7102
Non-polymers7422
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.245, 90.448, 130.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Indoleamine 2,3-dioxygenase 1 / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase


Mass: 44355.102 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-QPV / 3-chloro-N-{4-[1-(propylcarbamoyl)cyclobutyl]phenyl}benzamide


Mass: 370.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: from commercial screen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→74.25 Å / Num. obs: 93269 / % possible obs: 96.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.138 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.034 / Χ2: 0.965 / Net I/σ(I): 24.82
Reflection shellResolution: 1.78→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.326 / Num. unique obs: 323 / CC1/2: 1 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.78→74.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.083 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 2453 2.6 %RANDOM
Rwork0.192 ---
obs0.1927 90816 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121 Å2 / Biso mean: 34.988 Å2 / Biso min: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å2-0 Å2-0 Å2
2--0.84 Å2-0 Å2
3---1.06 Å2
Refinement stepCycle: final / Resolution: 1.78→74.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5969 0 52 520 6541
Biso mean--23.52 41.21 -
Num. residues----753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196261
X-RAY DIFFRACTIONr_bond_other_d0.0030.026010
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9748499
X-RAY DIFFRACTIONr_angle_other_deg1.179313832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92524.182275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6131533
X-RAY DIFFRACTIONr_chiral_restr0.080.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021455
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 180 -
Rwork0.314 6572 -
all-6752 -
obs--95.96 %

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