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- PDB-6azw: IDO1/FXB-001116 crystal structure -

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Basic information

Entry
Database: PDB / ID: 6azw
TitleIDO1/FXB-001116 crystal structure
ComponentsIndoleamine 2,3-dioxygenase 1
Keywordsoxidoreductase/oxidoreductase inhibitor / IDO1/FXB-001116 crystal structure / oxidoreductase-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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #480 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C51 / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.78 Å
AuthorsLewis, H.A. / Lammens, A. / Steinbacher, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Immune-modulating enzyme indoleamine 2,3-dioxygenase is effectively inhibited by targeting its apo-form.
Authors: Nelp, M.T. / Kates, P.A. / Hunt, J.T. / Newitt, J.A. / Balog, A. / Maley, D. / Zhu, X. / Abell, L. / Allentoff, A. / Borzilleri, R. / Lewis, H.A. / Lin, Z. / Seitz, S.P. / Yan, C. / Groves, J.T.
History
DepositionSep 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 16, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible

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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)89,4774
Polymers88,7102
Non-polymers7672
Water0
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


  • defined by author&software
  • 44.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,7392
Polymers44,3551
Non-polymers3831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


  • defined by author&software
  • 44.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,7392
Polymers44,3551
Non-polymers3831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.206, 92.555, 128.698
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: 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-C51 / (2R)-N-(4-cyanophenyl)-2-[cis-4-(quinolin-4-yl)cyclohexyl]propanamide


Mass: 383.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N3O

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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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 16% PEG 8K, 0.2 M NH4 acetate, 0.1 M CHES pH 8.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→46.278 Å / Num. obs: 25234 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.661 % / Biso Wilson estimate: 70.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.053 / Χ2: 1.079 / Net I/σ(I): 18.67 / Num. measured all: 92390 / Scaling rejects: 541
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.78-3.033.760.4353.1556700.9190.50696.4
3.03-3.343.5450.2036.3948730.9710.23895.6
3.34-3.843.8550.08414.8849760.9940.09797.6
3.84-4.683.5340.03825.9342750.9980.04595.3
4.68-5.933.6420.02836.3326870.9990.03294.8
5.93-7.623.5920.02344.0114110.9990.02795.7
7.62-11.113.540.01755.5389810.0297.3
11.11-17.793.2850.01461.733330.9990.01793.3
17.79-46.2783.4410.01664.5611110.01988.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.78→46.278 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2986 739 2.93 %
Rwork0.2166 --
obs0.2191 25191 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→46.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5655 0 58 0 5713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165854
X-RAY DIFFRACTIONf_angle_d1.4627967
X-RAY DIFFRACTIONf_dihedral_angle_d11.7093501
X-RAY DIFFRACTIONf_chiral_restr0.067910
X-RAY DIFFRACTIONf_plane_restr0.0121056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.99460.45111280.32384840X-RAY DIFFRACTION96
2.9946-3.29590.39781460.30614772X-RAY DIFFRACTION95
3.2959-3.77260.36471500.23424949X-RAY DIFFRACTION98
3.7726-4.75240.23741570.19864844X-RAY DIFFRACTION95
4.7524-46.28390.271580.18435047X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.72831.38161.33883.20620.55093.1292-0.1580.53320.12160.070.0835-0.6402-0.18170.6007-0.36660.4556-0.0487-0.01480.40240.120.656848.4604-23.436489.8756
24.76191.66371.69991.2180.24992.29840.03950.1369-0.08280.1852-0.1450.0080.16030.1238-0.08870.46720.0346-0.00950.33840.00270.514933.6529-32.739689.3959
35.43952.97792.54812.57430.72454.1946-0.4954-0.80331.1022-0.2384-0.08440.3963-0.0139-0.885-0.01280.4022-0.0255-0.16750.4701-0.11350.751422.277-26.003887.809
42.47460.97791.58253.1240.46293.6384-0.1672-0.04620.4282-0.1287-0.28830.2858-0.282-0.3572-0.2650.3858-0.0494-0.0660.4112-0.03720.583818.7346-30.121985.7377
58.8589-1.19395.56814.07460.96284.2796-0.5498-2.0150.77190.5405-0.52360.7558-0.4452-1.4007-0.55360.6921-0.21790.1391.1029-0.05710.586120.0363-30.9039101.6336
66.4849-1.2804-1.42873.1092-1.7222.6510.41971.85470.6531-0.4434-0.38530.4787-0.2722-1.881-0.47330.6918-0.00240.06341.0388-0.13680.59589.402-6.354767.5881
70.493-0.96921.23453.2253-3.36873.8728-0.42811.1061-0.86580.60470.07220.9339-0.7567-0.6469-0.43160.36770.05830.10791.8124-0.23511.4407-8.46381.423383.6649
82.71781.12342.78634.63270.8582.9222-0.37850.0597-1.6937-0.3518-0.40881.38790.2271-1.34460.15010.6809-0.31420.16911.5018-0.29261.2831-8.3699-6.887186.1495
93.8197-0.9794-1.43624.01850.98917.1548-0.12510.1668-0.59530.4735-0.39410.7530.3623-2.0391-0.21590.4423-0.07920.12460.8616-0.05860.63711.2127-2.350788.0722
104.5506-0.7808-0.58852.24850.71365.31840.17730.95040.406-0.2037-0.6754-0.0024-0.0732-1.0872-0.58450.47940.15040.04070.8556-0.07340.75574.60840.685577.9155
113.08350.2911-2.18751.64240.21134.12630.4480.97370.3977-0.6124-0.2649-0.0621-0.2808-0.6895-0.01220.460.11110.0440.67420.09530.401425.00931.606667.2133
123.9405-0.95140.23374.02660.62994.3666-0.0648-0.7088-0.05781.4575-0.19010.5437-0.3381-0.3167-0.07380.607-0.0490.1260.8404-0.0710.33128.4311-0.750694.0518
131.8251-0.7903-0.4381.5757-0.44582.62410.0366-0.0624-0.20260.0815-0.0663-0.07940.26140.0704-0.05480.4750.08690.04610.4566-0.07510.463127.8291-4.193477.3747
144.2695-2.558-2.15274.81111.93575.02950.0924-0.60761.11650.17490.5395-0.7806-0.19410.0554-0.19340.57360.0034-0.09270.5609-0.17810.782528.82396.026687.7807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 286 )
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 353 )
5X-RAY DIFFRACTION5chain 'A' and (resid 354 through 401 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 33 )
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 52 )
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 72 )
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 104 )
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 159 )
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 219 )
12X-RAY DIFFRACTION12chain 'B' and (resid 220 through 258 )
13X-RAY DIFFRACTION13chain 'B' and (resid 259 through 353 )
14X-RAY DIFFRACTION14chain 'B' and (resid 354 through 401 )

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