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- PDB-5xe1: Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) co... -

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Basic information

Entry
Database: PDB / ID: 5xe1
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with INCB14943
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / IDO1 / INCB14943
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / indoleamine 2,3-dioxygenase activity / smooth muscle contractile fiber / kynurenic acid biosynthetic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / 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 / smooth muscle contractile fiber / kynurenic acid biosynthetic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-IUU / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsXu, J. / Wu, U. / Liu, J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural insights into the binding mechanism of IDO1 with hydroxylamidine based inhibitor INCB14943
Authors: Wu, Y. / Xu, T. / Liu, J. / Ding, K. / Xu, J.
History
DepositionMar 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)92,5456
Polymers90,7682
Non-polymers1,7764
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-44 kcal/mol
Surface area30970 Å2
2
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2723
Polymers45,3841
Non-polymers8882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-21 kcal/mol
Surface area15930 Å2
MethodPISA
3
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2723
Polymers45,3841
Non-polymers8882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-20 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.050, 97.380, 128.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 12 - 400 / Label seq-ID: 12 - 400

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
2
1

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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-IUU / 4-Amino-N-(3-chloro-4-fluorophenyl)-N'-hydroxy-1,2,5-oxadiazole-3-carboxamidine


Mass: 271.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7ClFN5O2
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 Å3/Da / Density % sol: 58.99 % / Mosaicity: 1.16 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 10% (w/v) PEG-8000, 0.1M CHES pH 9.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.2→97.38 Å / Num. obs: 18282 / % possible obs: 98.4 % / Redundancy: 6.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.057 / Rrim(I) all: 0.157 / Net I/σ(I): 8.7 / Num. measured all: 122125 / Scaling rejects: 370
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.2-3.4260.891936132120.7120.3790.973297.6
9.05-97.386.40.05758369080.9970.0220.06120.798.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EK3

5ek3


Resolution: 3.2→25 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 65.181 / SU ML: 0.473 / Cross valid method: THROUGHOUT / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27432 931 5.1 %RANDOM
Rwork0.22781 ---
obs0.23015 17190 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.162 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2---3.64 Å20 Å2
3---4.17 Å2
Refinement stepCycle: 1 / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 122 0 6010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196165
X-RAY DIFFRACTIONr_bond_other_d0.0070.025922
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9948360
X-RAY DIFFRACTIONr_angle_other_deg1.379313617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2085734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41824.126269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.585151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3111532
X-RAY DIFFRACTIONr_chiral_restr0.0850.2907
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216898
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021444
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0876.0182954
X-RAY DIFFRACTIONr_mcbond_other1.0876.0192953
X-RAY DIFFRACTIONr_mcangle_it1.9029.0253682
X-RAY DIFFRACTIONr_mcangle_other1.9029.0253683
X-RAY DIFFRACTIONr_scbond_it1.1826.2063211
X-RAY DIFFRACTIONr_scbond_other1.1816.2053210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7259.2744678
X-RAY DIFFRACTIONr_long_range_B_refined6.07757.63226107
X-RAY DIFFRACTIONr_long_range_B_other6.07757.63426108
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 45994 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 67 -
Rwork0.344 1243 -
obs--98.05 %
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)
14.9802-0.8158-2.35541.2820.37121.9931-0.01570.0208-0.156-0.0168-0.09140.0053-0.0186-0.11860.10710.09630.03090.01470.04570.06740.2558-9.892129.4883-26.1009
24.715-0.753-5.3860.37941.833615.0889-0.24120.8509-0.2604-0.1793-0.19970.14850.1887-0.33140.44090.4390.0386-0.06540.4191-0.04880.3184-30.543829.1608-33.2388
33.7242-0.12531.0391.75291.06812.48760.00380.0194-0.0782-0.0469-0.26550.4243-0.069-0.54350.26180.112-0.04720.0280.1755-0.08940.2711-28.76960.4637-14.6334
41.27670.7156-1.24268.79093.94433.8232-0.1856-0.08240.0791-0.21640.337-0.10710.17190.4217-0.15130.22470.10380.04760.4025-0.01150.2052-8.0618-2.3948-20.5464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 360
2X-RAY DIFFRACTION2A382 - 401
3X-RAY DIFFRACTION3B12 - 361
4X-RAY DIFFRACTION4B380 - 401

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