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- PDB-6kps: Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in com... -

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Basic information

Entry
Database: PDB / ID: 6kps
TitleCrystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in complex with compound 36
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/INHIBITOR / tryptophan catabolism / heme / iron / metal binding / kynurenine / immunity / OXIDOREDUCTASE-INHIBITOR complex
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-DU6 / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsPeng, Y.H. / Wu, S.Y.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Unique Sulfur-Aromatic Interactions Contribute to the Binding of Potent Imidazothiazole Indoleamine 2,3-Dioxygenase Inhibitors.
Authors: Peng, Y.H. / Liao, F.Y. / Tseng, C.T. / Kuppusamy, R. / Li, A.S. / Chen, C.H. / Fan, Y.S. / Wang, S.Y. / Wu, M.H. / Hsueh, C.C. / Chang, J.Y. / Lee, L.C. / Shih, C. / Shia, K.S. / Yeh, T.K. ...Authors: Peng, Y.H. / Liao, F.Y. / Tseng, C.T. / Kuppusamy, R. / Li, A.S. / Chen, C.H. / Fan, Y.S. / Wang, S.Y. / Wu, M.H. / Hsueh, C.C. / Chang, J.Y. / Lee, L.C. / Shih, C. / Shia, K.S. / Yeh, T.K. / Hung, M.S. / Kuo, C.C. / Song, J.S. / Wu, S.Y. / Ueng, S.H.
History
DepositionAug 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)92,7246
Polymers90,7682
Non-polymers1,9564
Water1,29772
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3623
Polymers45,3841
Non-polymers9782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-23 kcal/mol
Surface area15890 Å2
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3623
Polymers45,3841
Non-polymers9782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-23 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.693, 92.555, 130.661
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: 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 / Plasmid: pET14b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DU6 / 1-(4-cyanophenyl)-3-[[3-(2-cyclopropylethynyl)imidazo[2,1-b][1,3]thiazol-5-yl]methyl]urea


Mass: 361.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15N5OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, Ammonium Fluoride, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: May 26, 2017
Details: Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.249→30 Å / Num. obs: 47893 / % possible obs: 96.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Χ2: 1.038 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.333.10.55947380.8390.3620.671.0996.7
2.33-2.423.30.40847940.9180.2520.4821.07397.5
2.42-2.533.30.31147920.9430.1910.3671.05997.9
2.53-2.673.40.22348440.9620.1380.2641.00598
2.67-2.833.40.14848060.9820.0930.1751.02997.5
2.83-3.053.30.10347920.9890.0650.1221.05596.8
3.05-3.363.30.06947890.9940.0440.0821.01996.4
3.36-3.853.30.04948080.9950.0320.0591.03395.9
3.85-4.843.30.03947650.9970.0250.0471.01794.5
4.84-4.843.30.03347650.9980.0210.0391.00790.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EK3

5ek3


Resolution: 2.249→29.744 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.2426 2435 5.09 %
Rwork0.2038 --
obs0.2058 47849 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.98 Å2 / Biso mean: 56.2609 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.249→29.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5872 0 138 72 6082
Biso mean--46.62 54.37 -
Num. residues----743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.249-2.29450.3361140234985
2.2945-2.34430.3522141265097
2.3443-2.39880.3619125270497
2.3988-2.45880.2969158270098
2.4588-2.52520.3031164269998
2.5252-2.59950.2913143269698
2.5995-2.68340.2721149271698
2.6834-2.77920.2988159267497
2.7792-2.89040.2763150270197
2.8904-3.02180.2632134271397
3.0218-3.1810.2864133268896
3.181-3.380.3015146268596
3.38-3.64050.2822142271096
3.6405-4.00610.2373119270596
4.0061-4.5840.18151310.1647269295
4.584-5.76850.20821710.1723264793
5.7685-29.7440.18011300.1569268589

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