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- PDB-6pz1: Crystal Structure of human Indoleamine 2,3-Dioxygenase 1 in compl... -

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Basic information

Entry
Database: PDB / ID: 6pz1
TitleCrystal Structure of human Indoleamine 2,3-Dioxygenase 1 in complex with PF-06840003 in Active Site and Si site
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOxidoreductase/Oxidoreductase inhibitor / Indoamine 2 / 3-Dioxygenase / PF-06840003 / Oxidoreductase / Oxidoreductase-Oxidoreductase inhibitor complex
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 / stereocilium bundle / tryptophan catabolic process to kynurenine / 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 / stereocilium bundle / tryptophan catabolic process to kynurenine / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / 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 / negative regulation of T cell proliferation / 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-AOJ / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPham, K.N. / Lewis-Ballester, A. / 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: 2019
Title: Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase.
Authors: Pham, K.N. / Lewis-Ballester, A. / Yeh, S.R.
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)97,97412
Polymers95,5842
Non-polymers2,39010
Water3,387188
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7334
Polymers47,7921
Non-polymers9413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2418
Polymers47,7921
Non-polymers1,4497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.479, 97.858, 131.966
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: 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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AOJ / (3R)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione


Mass: 232.210 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H9FN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 10
Details: 100 mM Sodium thiosulfate, 100 mM CAPS buffer pH 10.0, and 20% (w/v) PEG 8000

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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: Feb 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.65→78.61 Å / Num. obs: 33561 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.99 / Net I/σ(I): 7.4
Reflection shellResolution: 2.65→2.79 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4816 / CC1/2: 0.54 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WMU

5wmu


Resolution: 2.65→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 20.772 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.585 / ESU R Free: 0.325
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 1671 5 %RANDOM
Rwork0.2201 ---
obs0.2225 31777 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.4 Å2 / Biso mean: 83.542 Å2 / Biso min: 50.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å2-0 Å2
2---3.47 Å20 Å2
3---5.23 Å2
Refinement stepCycle: final / Resolution: 2.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5963 0 167 188 6318
Biso mean--88.81 73.62 -
Num. residues----753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136284
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175869
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.6748527
X-RAY DIFFRACTIONr_angle_other_deg1.0881.59413619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51122.673303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.762151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.191532
X-RAY DIFFRACTIONr_chiral_restr0.0520.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026945
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021325
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 127 -
Rwork0.388 2269 -
all-2396 -
obs--99.25 %

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