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- PDB-6e40: Crystal structure of the indoleamine 2,3-dioxygenase 1 (IDO1) in ... -

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Basic information

Entry
Database: PDB / ID: 6.0E+40
TitleCrystal structure of the indoleamine 2,3-dioxygenase 1 (IDO1) in complexed with ferric heme and Epacadostat
ComponentsIndoleamine 2,3-dioxygenase 1
Keywordsoxidoreductase/oxidoreductase inhibitor / IDO1 / Epacadostat / inhibitor complex / 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
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-BBJ / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.306 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form.
Authors: Luo, S. / Xu, K. / Xiang, S. / Chen, J. / Chen, C. / Guo, C. / Tong, Y. / Tong, L.
History
DepositionJul 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: Indoleamine 2,3-dioxygenase 1
D: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,98411
Polymers181,2044
Non-polymers3,7817
Water3,117173
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3563
Polymers45,3011
Non-polymers1,0552
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)46,3563
Polymers45,3011
Non-polymers1,0552
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)45,9172
Polymers45,3011
Non-polymers6161
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)46,3563
Polymers45,3011
Non-polymers1,0552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.367, 200.144, 114.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 45300.898 Da / Num. of mol.: 4 / Fragment: residue 15-403 / Mutation: K116A, K117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BBJ / N-(3-bromo-4-fluorophenyl)-N'-hydroxy-4-{[2-(sulfamoylamino)ethyl]amino}-1,2,5-oxadiazole-3-carboximidamide


Mass: 438.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H13BrFN7O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.2 / Details: 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.306→46.857 Å / Num. obs: 81202 / % possible obs: 98.8 % / Redundancy: 3.755 % / Biso Wilson estimate: 49.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 1.158 / Net I/σ(I): 11.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.453.8930.7321.72129080.8050.84698.4
2.45-2.623.8220.4542.7122620.9150.52799.7
2.62-2.833.5890.2674.33113550.9630.31398.6
2.83-3.13.8610.157.69105970.9880.17399.5
3.1-3.463.8690.08512.9895700.9950.09999.4
3.46-3.993.6340.04920.9184630.9980.05898.7
3.99-4.883.6390.03628.4771170.9980.04297.8
4.88-6.863.7180.03329.1156850.9990.03899
6.86-46.8573.4790.02735.6232450.9990.03195.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.306→46.857 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.63
RfactorNum. reflection% reflection
Rfree0.2537 4029 4.97 %
Rwork0.2077 --
obs0.21 81122 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.17 Å2 / Biso mean: 55.8913 Å2 / Biso min: 30.43 Å2
Refinement stepCycle: final / Resolution: 2.306→46.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11735 0 247 173 12155
Biso mean--60.45 51.6 -
Num. residues----1486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312292
X-RAY DIFFRACTIONf_angle_d1.216706
X-RAY DIFFRACTIONf_chiral_restr0.0721799
X-RAY DIFFRACTIONf_plane_restr0.0072118
X-RAY DIFFRACTIONf_dihedral_angle_d22.4494468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3061-2.33320.37881220.31012366248889
2.3332-2.36170.37291470.29732642278999
2.3617-2.39160.30871470.29362613276099
2.3916-2.4230.3071340.280326882822100
2.423-2.45620.31231320.275526492781100
2.4562-2.49130.32241250.269226922817100
2.4913-2.52850.34921250.272126312756100
2.5285-2.5680.32481450.278226752820100
2.568-2.61010.28871410.263526282769100
2.6101-2.65510.35081370.258226812818100
2.6551-2.70340.29791400.257726632803100
2.7034-2.75540.30051410.25182662280399
2.7554-2.81160.31691170.26242597271497
2.8116-2.87270.28981490.24782613276297
2.8727-2.93960.29981280.239426492777100
2.9396-3.01310.26531370.242826782815100
3.0131-3.09450.30021490.245226822831100
3.0945-3.18550.34631270.23922696282399
3.1855-3.28830.28521630.232126372800100
3.2883-3.40580.27651230.22252701282499
3.4058-3.54220.2861400.2182659279999
3.5422-3.70330.26451530.20782693284699
3.7033-3.89850.23781430.19292628277198
3.8985-4.14260.22151550.17122587274296
4.1426-4.46220.20321570.16692677283499
4.4622-4.91080.20161560.16527082864100
4.9108-5.62040.22081300.17762729285999
5.6204-7.07720.2191400.19082773291399
7.0772-46.86680.18811260.16232796292295

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