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- PDB-8abx: Crystal structure of IDO1 in complex with Apoxidole-1 -

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Basic information

Entry
Database: PDB / ID: 8abx
TitleCrystal structure of IDO1 in complex with Apoxidole-1
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Heme-binding protein / natural product / Indoleamine 2 / 3-dioxygenase 1
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
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-N2U / Chem-N39 / TRIETHYLENE GLYCOL / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsDotsch, L. / Ziegler, S. / Waldmann, H. / Gasper, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other governmentEFRE-0200481 Germany
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Identification of a Novel Pseudo-Natural Product Type IV IDO1 Inhibitor Chemotype.
Authors: Davies, C. / Dotsch, L. / Ciulla, M.G. / Hennes, E. / Yoshida, K. / Gasper, R. / Scheel, R. / Sievers, S. / Strohmann, C. / Kumar, K. / Ziegler, S. / Waldmann, H.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Identification of a Novel Pseudo-Natural Product Type IV IDO1 Inhibitor Chemotype
Authors: Davies, C. / Dotsch, L. / Gessica Ciulla, M. / Hennes, E. / Yoshida, K. / Gasper, R. / Scheel, R. / Sievers, S. / Strohmann, C. / Kumar, K. / Ziegler, S. / Waldmann, H.
History
DepositionJul 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 5, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,54610
Polymers45,3671
Non-polymers2,1799
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint26 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.480, 109.490, 36.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 45367.156 Da / Num. of mol.: 1 / Fragment: Apo protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pGex6p / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase

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Non-polymers , 5 types, 150 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-N39 / O1-tert-butyl O2-ethyl O5-methyl (E,5R)-5-(1-methylindol-2-yl)-5-[(4-methylphenyl)sulfonylamino]pent-2-ene-1,2,5-tricarboxylate / 3-formyl rifamycin SV


Mass: 596.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H36N2O8S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-N2U / O2-tert-butyl O3-ethyl O6-methyl (2S,6R)-6-(1-methylindol-2-yl)-2,5-dihydro-1H-pyridine-2,3,6-tricarboxylate


Mass: 442.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N2O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 40% PEG200, 100mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→38.17 Å / Num. obs: 51920 / % possible obs: 99.6 % / Redundancy: 5.586 % / Biso Wilson estimate: 26.37 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.157 / Χ2: 0.853 / Net I/σ(I): 6.34 / Num. measured all: 290033 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.695.7081.4520.9121399376937490.4081.59799.5
1.69-1.745.6171.1381.220816371337060.5531.25399.8
1.74-1.795.5630.8231.719886358635750.7140.90899.7
1.79-1.845.4230.6572.1418917349734880.790.72699.7
1.84-1.915.0980.4752.8517353342934040.870.52999.3
1.91-1.975.3960.3793.7217563326632550.9230.41999.7
1.97-2.055.5510.2874.7917668318531830.9520.31699.9
2.05-2.135.9270.2396.0618203307430710.9670.26199.9
2.13-2.225.9510.2047.1617347292529150.9720.22499.7
2.22-2.335.9130.1867.9716556281628000.9710.20399.4
2.33-2.465.8370.1718.615767270527010.9730.18799.9
2.46-2.615.7850.1539.5214827257325630.9780.16899.6
2.61-2.795.7230.1410.2213586239023740.980.15499.3
2.79-3.015.6110.13110.9412597225422450.9790.14499.6
3.01-3.35.2020.1211.310835208920830.980.13499.7
3.3-3.695.0630.11112.149468188018700.980.12399.5
3.69-4.265.4820.11213.269187168016760.9830.12499.8
4.26-5.225.7740.11613.788390145614530.9780.12799.8
5.22-7.385.60.11213.376356114211350.9830.12499.4
7.38-38.174.9140.11112.7933126826740.980.12598.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.05 Å48.71 Å
Translation6.05 Å48.71 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487_4487refinement
XDS20220220data reduction
XSCALE20220220data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4x60

4x60


Resolution: 1.65→38.17 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2596 5 %
Rwork0.192 49318 -
obs0.193 51914 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.03 Å2 / Biso mean: 33.6008 Å2 / Biso min: 16.11 Å2
Refinement stepCycle: final / Resolution: 1.65→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 400 141 3494
Biso mean--51.53 35.4 -
Num. residues----369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.680.41281320.42362515264799
1.68-1.710.37011340.360125542688100
1.71-1.750.35351360.31125862722100
1.75-1.790.27391340.268625452679100
1.79-1.830.25651360.248525732709100
1.83-1.870.27671330.231825322665100
1.87-1.920.26331360.22742582271899
1.92-1.980.23111350.219725562691100
1.98-2.040.23281360.200525872723100
2.04-2.120.19751360.186725992735100
2.12-2.20.22161350.174325452680100
2.2-2.30.2131360.17632595273199
2.3-2.420.19661380.173926152753100
2.42-2.570.20271370.178425992736100
2.57-2.770.21041360.17462584272099
2.77-3.050.18431380.185526312769100
3.05-3.490.23931380.195626242762100
3.49-4.40.1641410.160326742815100
4.4-38.170.19621490.19032822297199

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