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- PDB-6mq6: Mapping the binding trajectory of a suicide inhibitor in human in... -

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Basic information

Entry
Database: PDB / ID: 6mq6
TitleMapping the binding trajectory of a suicide inhibitor in human indoleamine 2,3-dioxygenase 1
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / indoleamine 2 / 3-dioxygenase / heme-containing enzyme / BMS-986205 / structure-based design / hIDO1-selective inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / OXYGEN BINDING
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / positive regulation of T cell apoptotic process / negative 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
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-H7P / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsPham, K.N. / Yeh, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115773 United States
National Science Foundation (NSF, United States)CHE-1404929 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Mapping the Binding Trajectory of a Suicide Inhibitor in Human Indoleamine 2,3-Dioxygenase 1.
Authors: Pham, K.N. / Yeh, S.R.
History
DepositionOct 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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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)97,16410
Polymers95,5842
Non-polymers1,5808
Water2,666148
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5934
Polymers47,7921
Non-polymers8013
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)48,5716
Polymers47,7921
Non-polymers7795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.327, 96.407, 129.931
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: 47791.918 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 (E. coli) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-H7P / (2R)-N-(4-chlorophenyl)-2-[cis-4-(6-fluoroquinolin-4-yl)cyclohexyl]propanamide


Mass: 410.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24ClFN2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 10
Details: 100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 200 mM sodium chloride, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 15, 2018
RadiationMonochromator: double crystal diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.05→29.5 Å / Num. obs: 21005 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Net I/σ(I): 11.8
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3016 / CC1/2: 0.724 / Rpim(I) all: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WN8

5wn8


Resolution: 3.05→29 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 20.839 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22898 1094 5.2 %RANDOM
Rwork0.18394 ---
obs0.18629 19862 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 110.563 Å2
Baniso -1Baniso -2Baniso -3
1--3.7 Å2-0 Å2-0 Å2
2---0.28 Å20 Å2
3---3.98 Å2
Refinement stepCycle: 1 / Resolution: 3.05→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5858 0 108 148 6114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0146107
X-RAY DIFFRACTIONr_bond_other_d00.0175609
X-RAY DIFFRACTIONr_angle_refined_deg0.521.6698266
X-RAY DIFFRACTIONr_angle_other_deg0.6981.65313123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0085733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10822.625301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.238151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2561532
X-RAY DIFFRACTIONr_chiral_restr0.0260.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026744
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021151
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_it5.40111.2872944
X-RAY DIFFRACTIONr_mcbond_other5.411.2872945
X-RAY DIFFRACTIONr_mcangle_it8.6316.9253673
X-RAY DIFFRACTIONr_mcangle_other8.62916.9273674
X-RAY DIFFRACTIONr_scbond_it4.53511.6593163
X-RAY DIFFRACTIONr_scbond_other4.53411.6593163
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.55217.3384594
X-RAY DIFFRACTIONr_long_range_B_refined11.8511.897234
X-RAY DIFFRACTIONr_long_range_B_other11.8511.897234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 77 -
Rwork0.295 1416 -
obs--100 %

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