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

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Basic information

Entry
Database: PDB / ID: 5wmx
TitleStructural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1
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 / 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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / TRYPTOPHAN / 2-(1H-indol-3-yl)ethanol / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLewis-Ballester, A. / Yeh, S.R. / Pham, K.N. / Batabyal, D. / Karkashon, S. / Bonanno, J.B. / Poulos, T.M.
Funding support United States, 3items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)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_label_asym_id
Revision 1.3Nov 6, 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)97,41910
Polymers95,4042
Non-polymers2,0168
Water2,360131
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7105
Polymers47,7021
Non-polymers1,0084
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)48,7105
Polymers47,7021
Non-polymers1,0084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.057, 97.566, 130.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Indoleamine 2,3-dioxygenase 1 / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase


Mass: 47701.797 Da / Num. of mol.: 2 / Mutation: F270G
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

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Non-polymers , 5 types, 139 molecules

#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-ZCW / 2-(1H-indol-3-yl)ethanol


Mass: 161.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 10
Details: 100 mM Sodium thiosulfate, 100 mM pH 10.0 CAPS buffer, and 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
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.69→39.1 Å / Num. obs: 31517 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.033 / Net I/σ(I): 12.8
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 6 % / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4082 / CC1/2: 0.44 / Rpim(I) all: 0.85 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 2.69→39.1 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 36.34 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.719 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25415 1988 6.3 %RANDOM
Rwork0.21448 ---
obs0.21698 29358 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.372 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0 Å2
2---3.47 Å20 Å2
3---3.32 Å2
Refinement stepCycle: 1 / Resolution: 2.69→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 144 131 6263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196305
X-RAY DIFFRACTIONr_bond_other_d0.0010.025900
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.9928546
X-RAY DIFFRACTIONr_angle_other_deg0.853313686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0345755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64124.13276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.385151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5491534
X-RAY DIFFRACTIONr_chiral_restr0.0670.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021297
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_it0.8397.2143036
X-RAY DIFFRACTIONr_mcbond_other0.8397.2143036
X-RAY DIFFRACTIONr_mcangle_it1.52810.8063777
X-RAY DIFFRACTIONr_mcangle_other1.52810.8063778
X-RAY DIFFRACTIONr_scbond_it0.657.2553269
X-RAY DIFFRACTIONr_scbond_other0.657.2553270
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.12510.8584768
X-RAY DIFFRACTIONr_long_range_B_refined3.60183.5257025
X-RAY DIFFRACTIONr_long_range_B_other3.59583.4947023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.688→2.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 136 -
Rwork0.387 2021 -
obs--93.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3278-0.74911.73562.1411-0.80432.4302-0.0765-0.2527-0.06030.2514-0.117-0.5281-0.00170.41150.19350.13560.0493-0.020.24360.04820.1852201.208498.19915.8189
26.35611.5078-3.46821.0659-0.75252.671-0.0402-0.4195-0.29180.1228-0.144-0.0235-0.01440.33470.18430.1413-0.02330.01470.0908-0.05560.1442185.4181127.433527.1795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 503
2X-RAY DIFFRACTION2B13 - 503

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