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- PDB-5ek3: Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) co... -

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Basic information

Entry
Database: PDB / ID: 5ek3
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / 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 L-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 L-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 / 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-5PK / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.209 Å
AuthorsPeng, Y.H. / Wu, J.S. / Wu, S.Y.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1
Authors: Peng, Y.H. / Ueng, S.H. / Tseng, C.T. / Hung, M.S. / Song, J.S. / Wu, J.S. / Liao, F.Y. / Fan, Y.S. / Wu, M.H. / Hsiao, W.C. / Hsueh, C.C. / Lin, S.Y. / Cheng, C.Y. / Tu, C.H. / Lee, L.C. / ...Authors: Peng, Y.H. / Ueng, S.H. / Tseng, C.T. / Hung, M.S. / Song, J.S. / Wu, J.S. / Liao, F.Y. / Fan, Y.S. / Wu, M.H. / Hsiao, W.C. / Hsueh, C.C. / Lin, S.Y. / Cheng, C.Y. / Tu, C.H. / Lee, L.C. / Cheng, M.F. / Shia, K.S. / Shih, C. / Wu, S.Y.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 / diffrn_radiation_wavelength / 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
Revision 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5666
Polymers90,7682
Non-polymers1,7984
Water4,468248
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2833
Polymers45,3841
Non-polymers8992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-23 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2833
Polymers45,3841
Non-polymers8992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-23 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.745, 92.256, 129.638
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 / 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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-5PK / (1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol


Mass: 282.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG, Ammonium Fluoride / PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 50213 / % possible obs: 96.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 42.45 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.028 / Rrim(I) all: 0.061 / Χ2: 1.059 / Net I/av σ(I): 24.45 / Net I/σ(I): 14.2 / Num. measured all: 223304
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.40.55148870.8440.30.6291.07395.2
2.28-2.374.40.3648710.9110.1960.4111.09795
2.37-2.484.30.2849160.9480.1520.3191.09795.8
2.48-2.614.30.20249850.9680.110.2311.05296.4
2.61-2.774.30.13350320.9860.0720.1521.02197.7
2.77-2.994.50.08651310.9940.0450.0981.04699
2.99-3.294.50.06448030.9960.0330.0721.06692.4
3.29-3.764.60.04851820.9980.0240.0531.05499.5
3.76-4.734.70.03752420.9990.0180.0411.01499.4
4.73-304.50.03351640.9980.0160.0371.07893.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 2.209→19.822 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 2564 5.12 %
Rwork0.1839 47544 -
obs0.1864 50108 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.92 Å2 / Biso mean: 57.0304 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: final / Resolution: 2.209→19.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5944 0 128 248 6320
Biso mean--38.57 56.21 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046234
X-RAY DIFFRACTIONf_angle_d0.7248463
X-RAY DIFFRACTIONf_chiral_restr0.047914
X-RAY DIFFRACTIONf_plane_restr0.0041072
X-RAY DIFFRACTIONf_dihedral_angle_d16.0463707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2093-2.25170.37731270.33252427255489
2.2517-2.29760.33991400.28952558269895
2.2976-2.34750.30861520.25722551270395
2.3475-2.4020.30691440.25542608275295
2.402-2.4620.34251350.24112601273695
2.462-2.52840.2751210.23072614273596
2.5284-2.60270.26661360.2322621275796
2.6027-2.68650.25381390.22832669280897
2.6865-2.78230.30171390.21462674281398
2.7823-2.89330.24471590.22772672283199
2.8933-3.02460.30311340.222327282862100
3.0246-3.18340.32561470.2442379252687
3.1834-3.3820.28381480.21642695284399
3.382-3.64160.21331450.18812746289199
3.6416-4.00540.18681530.14892750290399
4.0054-4.57870.17731520.129127842936100
4.5787-5.74530.17071530.127528072960100
5.7453-19.82320.20221400.15282660280091
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)
13.9863-1.41512.09082.5499-0.79342.0347-0.00180.85210.8309-0.0084-0.6268-0.876-0.34121.22190.71360.4491-0.03880.04230.87790.24130.71945.21653.118414.8368
24.7847-0.4711.17193.4797-0.94345.0835-0.09160.44020.5732-0.0482-0.5062-0.5426-0.11180.86810.49160.27170.0001-0.02550.52950.14170.489339.66010.317517.808
35.7385-1.98654.73691.7649-1.99816.5610.21310.4089-0.0815-0.3201-0.26110.11180.24570.25630.0180.30870.03260.00990.3134-0.07480.330421.391-3.54719.34
47.0612-0.72452.96470.6775-1.57844.9689-0.1595-0.36460.96710.3803-0.0892-0.0818-0.61450.1680.23260.5870.0272-0.07280.3659-0.15950.6625.14127.92123.6813
53.7656-1.51681.91781.7423-0.6693.1878-0.0568-0.07180.3239-0.31740.02550.2991-0.2265-0.37380.08560.37820.0935-0.06980.3239-0.04060.350411.89362.29369.7495
65.5296-6.21722.2736.1146-4.01384.9698-0.0337-1.4746-0.95560.24730.89330.70990.006-0.9591-0.94030.37070.01390.00620.51510.10790.454512.4076-6.115123.2218
72.31782.7637-1.10144.97890.24193.9062-0.12190.86580.6702-0.75090.22010.4041-0.2273-0.5075-0.05560.3993-0.0031-0.08470.47440.01830.31423.241831.940613.5924
84.58640.73641.07075.1082.1649.0377-0.18250.3560.0185-0.1848-0.12330.8090.3199-0.77590.29130.2519-0.08930.01470.4442-0.06740.4769-13.006222.988628.6673
94.82910.0421-0.56165.3978-2.87934.8226-0.2915-0.0246-0.13040.1082-0.02710.11520.2252-0.45190.23370.308-0.06240.05340.2664-0.09660.2872-3.374921.498131.7732
104.0720.721-0.81424.7439-1.20572.3073-0.13990.28290.0964-0.33140.05720.21830.0189-0.42850.06770.2766-0.0336-0.02520.3376-0.05170.2132-0.650430.052624.5086
117.09560.6442-5.691-0.2034-0.20916.6001-0.10710.44570.3374-0.18540.1384-0.063-0.1381-0.0504-0.07270.4016-0.03030.01190.32950.03150.360519.30339.464517.142
124.33063.09380.36395.4349-0.69262.9297-0.0316-0.56830.14720.5432-0.09940.2520.10930.00110.11630.30310.00020.0160.3409-0.00560.22945.924928.286939.8188
134.0960.0112-1.78990.1012-0.28072.63210.06950.0003-0.44370.3265-0.0423-0.06070.1867-0.1048-0.08010.4681-0.02420.03040.2642-0.05550.45658.763317.554329.0029
146.29594.0632-4.10576.2939-5.14036.76710.0524-0.0089-0.754-0.0627-0.4133-0.51770.61120.65110.46120.45990.05990.05280.3496-0.05790.518421.656120.882125.5353
159.52673.48840.47185.48710.74971.0732-0.5310.8842-0.9369-0.6220.4032-0.63090.15020.10610.19980.4922-0.02150.10890.3799-0.04210.366925.764826.476212.7472
161.2675-0.26270.28611.8851-0.38791.6210.2339-0.21840.29040.0156-0.0998-0.1538-0.39770.4719-0.35370.3076-0.0512-0.00630.3309-0.04050.291926.012838.625127.0795
174.2405-3.2003-2.75362.52752.04137.7428-0.1557-1.2077-0.51140.4896-0.21060.09720.38040.79450.27280.3961-0.0694-0.05050.47140.01330.314323.67230.004336.739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 72 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 159 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 240 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 298 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 353 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 403 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 33 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 72 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 104 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 159 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 220 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 221 through 240 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 241 through 276 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 277 through 298 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 299 through 325 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 326 through 353 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 354 through 403 )B0

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