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- PDB-5wn8: Structural Insights into Substrate and Inhibitor Binding Sites in... -

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Basic information

Entry
Database: PDB / ID: 5wn8
TitleStructural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Indoleamine 2 / 3-Dioxygenase 1 Tryptophan Heme Inhibitor Epacadostat INCB024360
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
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
Chem-BBJ / PROTOPORPHYRIN IX CONTAINING FE / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLewis-Ballester, A. / Pham, K.N. / Batabyal, D. / Karkashon, S. / Bonanno, J.B. / Poulos, T.L. / Yeh, S.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM115773 United States
National Science Foundation (NSF, United States)CHE-1404929 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM57353 United States
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1.
Authors: Lewis-Ballester, A. / Pham, K.N. / Batabyal, D. / Karkashon, S. / Bonanno, J.B. / Poulos, T.L. / Yeh, S.R.
History
DepositionJul 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
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
Revision 1.3Oct 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)97,6936
Polymers95,5842
Non-polymers2,1094
Water2,666148
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8473
Polymers47,7921
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)48,8473
Polymers47,7921
Non-polymers1,0552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.735, 97.785, 128.739
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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 2 / Source method: obtained synthetically / Formula: C11H13BrFN7O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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 / 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: 9.5
Details: 100 mM Sodium thiosulfate, 100 mM CAPS buffer pH 9.5, and 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.91988 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91988 Å / Relative weight: 1
ReflectionResolution: 2.5→29.69 Å / Num. obs: 38582 / % possible obs: 99.9 % / Redundancy: 14.8 % / CC1/2: 0.59 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.023 / Net I/σ(I): 22.5
Reflection shellResolution: 2.5→2.565 Å / Redundancy: 14.9 % / Rmerge(I) obs: 2.3 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5556 / CC1/2: 0.59 / Rpim(I) all: 0.61 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 2.5→29.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 11.624 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.263 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25182 1928 5 %RANDOM
Rwork0.21347 ---
obs0.21535 36596 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.291 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å2-0 Å2
2---2.05 Å20 Å2
3---3.42 Å2
Refinement stepCycle: 1 / Resolution: 2.5→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 136 148 6164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196169
X-RAY DIFFRACTIONr_bond_other_d0.0010.025742
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9968376
X-RAY DIFFRACTIONr_angle_other_deg0.872313314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2335737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92924.148270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.598151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6261532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216803
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021273
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_it2.0778.0942960
X-RAY DIFFRACTIONr_mcbond_other2.0768.0932959
X-RAY DIFFRACTIONr_mcangle_it3.48412.1353693
X-RAY DIFFRACTIONr_mcangle_other3.48312.1363694
X-RAY DIFFRACTIONr_scbond_it1.9928.3633209
X-RAY DIFFRACTIONr_scbond_other1.9928.3653210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.39712.4454684
X-RAY DIFFRACTIONr_long_range_B_refined8.34493.9816948
X-RAY DIFFRACTIONr_long_range_B_other8.33293.9436928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 162 -
Rwork0.344 2640 -
obs--100 %

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