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

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Basic information

Entry
Database: PDB / ID: 5wmu
TitleStructural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase I
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Dioxygenase Tryptophan Heme Inhibitor
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / TRYPTOPHAN / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLewis-Ballester, A. / Yeh, S.R. / Pham, K.N. / Batabyal, D. / Karkashon, S. / Bonanno, J.B. / Poulos, T.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)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.pdbx_value_order / _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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)97,2778
Polymers95,5842
Non-polymers1,6936
Water4,035224
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6394
Polymers47,7921
Non-polymers8473
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)48,6394
Polymers47,7921
Non-polymers8473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.301, 97.768, 125.643
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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 10
Details: 100 mM Sodium thiosulfate, 100 mM pH 10.0 CAPS buffer, 20% (w/v) PEG 8000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→38.7 Å / Num. obs: 43748 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 6 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2899 / CC1/2: 0.7 / Rpim(I) all: 0.52 / % possible all: 98.3

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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: 2.4→38.65 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.015 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25791 1994 4.6 %RANDOM
Rwork0.21404 ---
obs0.21604 41644 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.791 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å2-0 Å2
2---3.29 Å20 Å2
3---5.4 Å2
Refinement stepCycle: 1 / Resolution: 2.4→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 0 120 224 6346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196279
X-RAY DIFFRACTIONr_bond_other_d0.0010.025851
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9878517
X-RAY DIFFRACTIONr_angle_other_deg0.871313573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2465756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31324.182275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.126151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3931532
X-RAY DIFFRACTIONr_chiral_restr0.0660.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216928
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021290
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_it1.9057.7993044
X-RAY DIFFRACTIONr_mcbond_other1.9057.83043
X-RAY DIFFRACTIONr_mcangle_it3.2511.6913792
X-RAY DIFFRACTIONr_mcangle_other3.2511.6913793
X-RAY DIFFRACTIONr_scbond_it1.6747.9223235
X-RAY DIFFRACTIONr_scbond_other1.6747.9223235
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.85511.8044726
X-RAY DIFFRACTIONr_long_range_B_refined5.25189.9887149
X-RAY DIFFRACTIONr_long_range_B_other5.20989.9017118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 141 -
Rwork0.362 2899 -
obs--95.9 %

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