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- PDB-8i7l: Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) comple... -

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Basic information

Entry
Database: PDB / ID: 8i7l
TitleCrystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with a novel inhibitor
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsMETAL BINDING PROTEIN / 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 / stereocilium bundle / tryptophan catabolic process to kynurenine / 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 / stereocilium bundle / tryptophan catabolic process to kynurenine / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / positive regulation of T cell apoptotic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / negative regulation of T cell proliferation / 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-OIH / THIOSULFATE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, K. / Liu, W. / Dong, X.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81922067 China
National Natural Science Foundation of China (NSFC)21937005 China
National Natural Science Foundation of China (NSFC)21772233 China
National Natural Science Foundation of China (NSFC)81903620 China
CitationJournal: J Immunol. / Year: 2022
Title: Apo-Form Selective Inhibition of IDO for Tumor Immunotherapy.
Authors: Liu, W. / Zou, Y. / Li, K. / Zhong, H. / Yu, L. / Ge, S. / Lai, Y. / Dong, X. / Xu, Q. / Guo, W.
History
DepositionFeb 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)91,9355
Polymers90,7682
Non-polymers1,1663
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.110, 97.110, 128.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 45384.211 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 BL21(DE3) (bacteria) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2
#3: Chemical ChemComp-OIH / 1-[3-[(4-chloranyl-2-fluoranyl-phenyl)carbamoylamino]-4-[cyclohexyl(2-methylpropyl)amino]phenyl]pyrrole-2-carboxylic acid


Mass: 527.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H32ClFN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaS2O3, 0.1M CAPS (pH 10.3), 12% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.6 Å / Num. obs: 24091 / % possible obs: 87.63 % / Redundancy: 9.35 % / Rrim(I) all: 0.145 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.91 Å / Num. unique obs: 2576 / Rrim(I) all: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
SCALAdata scaling
XDSdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.555 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2933 1206 5.01 %
Rwork0.2702 --
obs0.2713 24090 87.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 79 30 5825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055932
X-RAY DIFFRACTIONf_angle_d0.9818025
X-RAY DIFFRACTIONf_dihedral_angle_d15.4393566
X-RAY DIFFRACTIONf_chiral_restr0.053879
X-RAY DIFFRACTIONf_plane_restr0.0061018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.41761360.41112576X-RAY DIFFRACTION90
2.9121-3.04470.41591360.40892582X-RAY DIFFRACTION90
3.0447-3.20510.40131350.38692563X-RAY DIFFRACTION90
3.2051-3.40590.32751330.34722547X-RAY DIFFRACTION89
3.4059-3.66880.34511340.3362528X-RAY DIFFRACTION87
3.6688-4.03780.33371310.28972490X-RAY DIFFRACTION87
4.0378-4.62170.27131340.2492551X-RAY DIFFRACTION88
4.6217-5.82130.29341330.23512532X-RAY DIFFRACTION86
5.8213-48.5550.21911340.20562515X-RAY DIFFRACTION82
Refinement TLS params.Method: refined / Origin x: 19.0991 Å / Origin y: 15.5087 Å / Origin z: 20.501 Å
111213212223313233
T0.5545 Å2-0.0436 Å2-0.0094 Å2-0.6803 Å2-0.026 Å2--0.6709 Å2
L1.3898 °2-0.3178 °2-0.4757 °2-1.3621 °20.2551 °2--1.0663 °2
S0.0616 Å °-0.1764 Å °0.1268 Å °0.0612 Å °-0.0932 Å °0.0035 Å °-0.0605 Å °0.2631 Å °0.023 Å °
Refinement TLS groupSelection details: all

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