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- PDB-4pk5: Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) co... -

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Basic information

Entry
Database: PDB / ID: 4pk5
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with Amg-1
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / indoleamine 2 / 3-dioxygenagse 1 / induced fit / structure based drug discovery / imidazothiazole / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle ... indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle / 'de novo' NAD+ biosynthetic process from L-tryptophan / positive regulation of type 2 immune response / L-tryptophan catabolic process / negative regulation of T cell apoptotic process / Tryptophan catabolism / 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-PKJ / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.79 Å
AuthorsKohno, T. / Tojo, S. / Ishii, T.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Crystal Structures and Structure-Activity Relationships of Imidazothiazole Derivatives as IDO1 Inhibitors.
Authors: Tojo, S. / Kohno, T. / Tanaka, T. / Kamioka, S. / Ota, Y. / Ishii, T. / Kamimoto, K. / Asano, S. / Isobe, Y.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1936
Polymers95,1112
Non-polymers2,0824
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-50 kcal/mol
Surface area30890 Å2
Unit cell
Length a, b, c (Å)84.799, 90.414, 131.757
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: 47555.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / 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-PKJ / N-(1,3-benzodioxol-5-yl)-2-{[5-(4-methylphenyl)[1,3]thiazolo[2,3-c][1,2,4]triazol-3-yl]sulfanyl}acetamide


Mass: 424.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N4O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% polyethylene glycol 20000, 2% Dioxane, 100 mM Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→74.56 Å / Num. obs: 25711 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 15
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.79→74.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.574 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 3.37 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25642 1255 4.9 %RANDOM
Rwork0.18499 ---
obs0.18849 24404 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å2-0 Å2
2--0.63 Å2-0 Å2
3---1.4 Å2
Refinement stepCycle: 1 / Resolution: 2.79→74.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5912 0 144 8 6064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196215
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.72528438
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67324.148270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.526151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9821532
X-RAY DIFFRACTIONr_chiral_restr0.1110.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214784
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.2795.5962980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.7158.3773718
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8355.9543235
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.10246.4489635
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.789→2.861 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 80 -
Rwork0.325 1579 -
obs--87.55 %

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