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

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Basic information

Entry
Database: PDB / ID: 5wmw
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 / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle ... indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle / 'de novo' NAD+ biosynthetic process from L-tryptophan / positive regulation of type 2 immune response / L-tryptophan catabolic process / negative regulation of T cell apoptotic process / Tryptophan catabolism / 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 / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 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 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_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 16, 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)97,50610
Polymers95,4042
Non-polymers2,1028
Water1,874104
1
A: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7535
Polymers47,7021
Non-polymers1,0514
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)48,7535
Polymers47,7021
Non-polymers1,0514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.192, 97.907, 127.863
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: 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
#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.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
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: Jun 3, 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: 3.03→39.08 Å / Num. obs: 21897 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 6 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.042 / Net I/σ(I): 14.1
Reflection shellResolution: 3.03→3.11 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4049 / CC1/2: 0.62 / Rpim(I) all: 0.55 / % possible all: 98.5

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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: 3.03→39.08 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 47.739 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25872 1996 9.1 %RANDOM
Rwork0.21172 ---
obs0.216 19850 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å2-0 Å2-0 Å2
2---4.71 Å20 Å2
3---2.9 Å2
Refinement stepCycle: 1 / Resolution: 3.03→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5999 0 150 104 6253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196306
X-RAY DIFFRACTIONr_bond_other_d0.0010.025892
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9878550
X-RAY DIFFRACTIONr_angle_other_deg0.848313670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9975756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78724.182275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.908151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3291532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216942
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021292
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_it0.7657.5033050
X-RAY DIFFRACTIONr_mcbond_other0.7657.5013049
X-RAY DIFFRACTIONr_mcangle_it1.38411.2393796
X-RAY DIFFRACTIONr_mcangle_other1.38411.2423797
X-RAY DIFFRACTIONr_scbond_it0.5087.5333256
X-RAY DIFFRACTIONr_scbond_other0.5087.5333256
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.95111.2894755
X-RAY DIFFRACTIONr_long_range_B_refined3.44287.2787103
X-RAY DIFFRACTIONr_long_range_B_other3.44187.2987104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.034→3.112 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 137 -
Rwork0.365 1380 -
obs--94.81 %
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)
13.4521-0.28571.08292.6099-0.51631.9672-0.1195-0.0721-0.03830.2421-0.1254-0.6873-0.00070.48910.24490.04360.04-0.02550.24430.05890.3795203.156698.5533143.3761
24.71970.943-2.43221.2136-0.44861.8510.0137-0.2715-0.12750.1179-0.1132-0.0498-0.07180.32850.09950.0212-0.0273-0.01440.099-0.04580.2329187.5981127.7736154.7252
300000000000000-00.2094000.209400.2094000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 503
2X-RAY DIFFRACTION2B13 - 502

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