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- PDB-6azv: IDO1/BMS-978587 crystal structure -

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Basic information

Entry
Database: PDB / ID: 6azv
TitleIDO1/BMS-978587 crystal structure
ComponentsIndoleamine 2,3-dioxygenase 1
Keywordsoxidoreductase/oxidoreductase inhibitor / IDO1 heme-displaced ligand-bound / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process ... indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle / positive regulation of type 2 immune response / L-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
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-C4V / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.755 Å
AuthorsLewis, H.A.
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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Indoleamine 2,3-dioxygenase 1
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,7708
Polymers181,0204
Non-polymers1,7504
Water1,910106
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6932
Polymers45,2551
Non-polymers4381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6932
Polymers45,2551
Non-polymers4381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6932
Polymers45,2551
Non-polymers4381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6932
Polymers45,2551
Non-polymers4381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)203.392, 120.868, 101.527
Angle α, β, γ (deg.)90.000, 119.110, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and resseq 501
21chain B and resseq 501
31chain C and resseq 501
41chain D and resseq 501
12(chain A and (resseq 11 or resseq 13:14 or (resid...
22(chain B and (resseq 11 or resseq 13:14 or (resid...
32(chain C and ((resid 11 and (name N or name...
42(chain D and (resseq 11 or resseq 13:14 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain TA1
211chain QB1
311chain RC1
411chain SD1
122(chain A and (resseq 11 or resseq 13:14 or (resid...A0
222(chain B and (resseq 11 or resseq 13:14 or (resid...B0
322(chain C and ((resid 11 and (name N or name...C0
422(chain D and (resseq 11 or resseq 13:14 or (resid...D0

NCS ensembles :
ID
1
2

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Components

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


Mass: 45254.988 Da / Num. of mol.: 4
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-C4V / (1R,2S)-2-(4-[bis(2-methylpropyl)amino]-3-{[(4-methylphenyl)carbamoyl]amino}phenyl)cyclopropane-1-carboxylic acid


Mass: 437.574 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H35N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 22% PEG-3350, 0.2 M NH4 citrate pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.755→45.405 Å / Num. all: 54682 / Num. obs: 54682 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 54.95 Å2 / Rpim(I) all: 0.076 / Rrim(I) all: 0.139 / Rsym value: 0.091 / Net I/av σ(I): 6.5 / Net I/σ(I): 10.5 / Num. measured all: 178933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.755-2.93.40.4271.680190.3250.6090.42799.7
2.9-3.083.50.3082.176130.2420.4560.30899.4
3.08-3.293.40.2422.671490.1930.3560.24299.5
3.29-3.563.20.1633.965790.1390.2520.16398.8
3.56-3.93.20.1016.160540.0890.1610.10197.9
3.9-4.3630.0728.954190.070.1230.07297
4.36-5.033.10.06110.547980.0540.0970.06197.3
5.03-6.163.20.0610.741230.0490.0880.0698.4
6.16-8.713.10.04513.331730.0340.0620.04597.7
8.71-45.4053.20.03615.817550.0260.0480.03696

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 2.755→45.108 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.96
RfactorNum. reflection% reflection
Rfree0.2719 2771 5.07 %
Rwork0.1947 --
obs0.1986 54642 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 467.55 Å2 / Biso mean: 68.3118 Å2 / Biso min: 23.65 Å2
Refinement stepCycle: final / Resolution: 2.755→45.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11078 0 268 318 11664
Biso mean--151.32 51.08 -
Num. residues----1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01611492
X-RAY DIFFRACTIONf_angle_d1.37315648
X-RAY DIFFRACTIONf_chiral_restr0.0671779
X-RAY DIFFRACTIONf_plane_restr0.012049
X-RAY DIFFRACTIONf_dihedral_angle_d12.3476849
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A0X-RAY DIFFRACTION6.046TORSIONAL
12B0X-RAY DIFFRACTION6.046TORSIONAL
13C0X-RAY DIFFRACTION6.046TORSIONAL
14D0X-RAY DIFFRACTION6.046TORSIONAL
21A6974X-RAY DIFFRACTION6.046TORSIONAL
22B6974X-RAY DIFFRACTION6.046TORSIONAL
23C6974X-RAY DIFFRACTION6.046TORSIONAL
24D6974X-RAY DIFFRACTION6.046TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7548-2.80230.37211400.29525912731100
2.8023-2.85330.36031440.29892597274199
2.8533-2.90810.39411350.29812630276599
2.9081-2.96750.33611640.274125652729100
2.9675-3.0320.34591120.25522665277799
3.032-3.10250.28861160.2432616273299
3.1025-3.18010.36481600.243525872747100
3.1801-3.2660.37751540.23352591274599
3.266-3.36210.33631490.22852609275899
3.3621-3.47060.25871250.21952577270298
3.4706-3.59460.29431350.21782600273599
3.5946-3.73840.30121280.19042572270098
3.7384-3.90850.26181310.1772567269897
3.9085-4.11440.27691530.1672551270497
4.1144-4.3720.21941510.15412552270397
4.372-4.70920.23081470.14972549269697
4.7092-5.18250.2191450.15062586273198
5.1825-5.9310.27811180.17712623274198
5.931-7.46690.24631410.1842622276398
7.4669-45.11380.20531230.17682621274496
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)
12.3272-0.0979-0.77980.72460.00751.6754-0.0513-0.50660.0642-0.01290.0379-0.2457-0.19490.7347-0.01130.3757-0.1175-0.07530.6729-0.14010.420349.943222.717-16.1632
23.00161.0123-2.43031.8522-0.04962.77580.00050.22640.1124-0.11640.0684-0.1807-0.02130.34370.09020.2623-0.08760.00250.3559-0.07470.323745.478722.2213-25.6424
33.4426-0.8314-1.76771.86110.36213.5593-0.244-0.12090.01950.50260.0593-0.3214-0.1130.3930.03820.2375-0.0499-0.02280.5155-0.10690.312146.273714.4137-21.0204
41.1520.0015-1.02260.508-0.58711.33760.0374-0.03050.14590.02660.04620.0343-0.13530.1537-0.09660.3025-0.0705-0.01670.4394-0.11250.343230.883920.3178-12.7969
53.83431.0162-2.15581.3586-0.68223.2345-0.27020.3434-0.3129-0.00390.0702-0.03750.2869-0.57030.120.3825-0.03950.07410.4621-0.14280.425126.31784.6179-9.1594
63.52073.7286-4.36077.8262-6.91136.3815-0.31440.4435-0.28020.30340.2013-0.2601-0.5127-0.61760.04120.3894-0.0568-0.02820.4776-0.01460.351915.635918.1139-10.2287
71.87543.5501-2.42066.4783-4.58024.2815-0.12450.2139-0.0095-0.5122-0.11750.04060.5923-0.08610.10180.3236-0.0678-0.0230.732-0.05820.384315.785717.0542-21.016
82.8266-2.17262.70065.311.1425.4826-0.0957-0.1652-0.5028-0.24360.0029-0.78060.00550.84420.09070.15790.0119-0.03260.57940.10280.528443.1065-17.0073-7.1939
90.80960.24710.58434.54071.54273.3833-0.1595-0.284-0.04540.91660.2003-0.38990.14440.5539-0.02780.53270.2073-0.10440.68940.05650.430133.8459-25.551113.9034
103.419-0.7651-1.89482.313-0.88895.38840.2269-0.26650.03980.4146-0.227-0.1832-0.02230.12980.03510.27660.0604-0.06450.30170.0030.327326.7217-22.17177.5734
114.1813-0.129-2.16383.03510.80768.74910.1483-0.13940.16490.1468-0.1087-0.2672-0.17960.1597-0.11990.29840.0263-0.0420.2786-0.0010.304631.0548-14.35365.8106
120.82940.2017-0.85030.7565-0.10882.6904-0.0593-0.0023-0.1893-0.0763-0.0597-0.1210.24750.06370.12950.32480.1082-0.03510.4902-0.01890.353531.5549-22.4339-11.6841
132.8329-0.0244-2.10780.7817-1.0814.97090.15520.150.1702-0.196-0.03470.038-0.3221-0.3532-0.26360.43690.09290.00330.4216-0.03370.347128.1284-7.198-15.115
144.58715.7083-6.03167.5415-7.57667.71840.0530.0221-0.1277-0.3281-0.2138-0.1530.2318-0.36520.28950.4430.0609-0.05250.6752-0.0180.349324.4755-18.3959-25.941
154.32074.0453-3.05658.83-6.56574.7310.0799-0.11950.40490.20970.1020.7632-0.2139-0.5539-0.33740.37010.09520.00480.7878-0.00570.343415.4262-17.4025-20.1993
164.5318-3.59330.41374.2182-1.27482.5235-0.4238-0.67220.09690.42880.1227-0.20430.0724-0.28380.20360.4897-0.07140.06520.3574-0.08790.322911.087321.384548.3282
173.9195-0.25550.94772.9044-0.90623.4736-0.1525-0.02220.2940.04650.02270.2407-0.1379-0.56470.16370.3004-0.0251-0.01840.4016-0.03250.3841-5.050333.795831.9146
181.8133-0.77580.22294.26550.46563.6513-0.04610.063-0.01860.2626-0.23680.15530.2417-0.30610.2550.2739-0.04320.03190.3445-0.08470.27861.926624.168335.3989
191.1886-0.10561.03061.8614-0.06461.80150.02320.4158-0.034-0.0899-0.0268-0.24980.28350.04210.12630.3262-0.01190.10660.325-0.02120.359614.831920.96831.5362
204.71-2.63510.77372.7866-0.64230.39480.13850.30940.18260.3182-0.512-0.84840.08190.10480.35070.3812-0.0999-0.07650.28610.02980.558326.890324.246239.6743
213.66271.68833.25741.50420.73054.39720.03040.0141-0.0832-0.13430.0175-0.42570.2960.00080.07110.3955-0.07880.12820.3038-0.12230.514724.481714.545224.1596
222.00271.14850.99122.10960.65191.6226-0.05790.4933-0.1623-0.32770.1366-0.0344-0.2756-0.18570.00170.42530.09040.01860.47530.05390.30865.7721-30.337522.786
235.88340.1306-1.29033.44740.93393.56590.52850.5533-0.697-0.0136-0.4788-0.1224-0.039-0.6004-0.00270.35710.0585-0.08610.3013-0.03230.43310.9964-39.295829.0978
241.80760.0973-0.24672.68480.38212.23210.18620.03860.2376-0.2763-0.0486-0.1374-0.5574-0.562-0.02020.53220.23310.0650.32540.06680.39515.7854-19.342927.5164
251.57950.27550.0931.12280.77380.95920.1048-0.15430.08320.12710.0132-0.1077-0.1571-0.1906-0.12370.50760.09860.02450.34280.07660.347113.3487-19.635743.909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 72 )A10 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 104 )A73 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 129 )A105 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 288 )A130 - 288
5X-RAY DIFFRACTION5chain 'A' and (resid 289 through 325 )A289 - 325
6X-RAY DIFFRACTION6chain 'A' and (resid 326 through 353 )A326 - 353
7X-RAY DIFFRACTION7chain 'A' and (resid 354 through 401 )A354 - 401
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 33 )B10 - 33
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 72 )B34 - 72
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 104 )B73 - 104
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 129 )B105 - 129
12X-RAY DIFFRACTION12chain 'B' and (resid 130 through 254 )B130 - 254
13X-RAY DIFFRACTION13chain 'B' and (resid 255 through 325 )B255 - 325
14X-RAY DIFFRACTION14chain 'B' and (resid 326 through 353 )B326 - 353
15X-RAY DIFFRACTION15chain 'B' and (resid 354 through 401 )B354 - 401
16X-RAY DIFFRACTION16chain 'C' and (resid 4 through 33 )C4 - 33
17X-RAY DIFFRACTION17chain 'C' and (resid 34 through 104 )C34 - 104
18X-RAY DIFFRACTION18chain 'C' and (resid 105 through 159 )C105 - 159
19X-RAY DIFFRACTION19chain 'C' and (resid 160 through 288 )C160 - 288
20X-RAY DIFFRACTION20chain 'C' and (resid 289 through 328 )C289 - 328
21X-RAY DIFFRACTION21chain 'C' and (resid 329 through 401 )C329 - 401
22X-RAY DIFFRACTION22chain 'D' and (resid 10 through 92 )D10 - 92
23X-RAY DIFFRACTION23chain 'D' and (resid 93 through 118 )D93 - 118
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 159 )D119 - 159
25X-RAY DIFFRACTION25chain 'D' and (resid 160 through 399 )D160 - 399

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