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- PDB-8vzv: Human TDO (hTDO) in complex with LM10 -

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Basic information

Entry
Database: PDB / ID: 8vzv
TitleHuman TDO (hTDO) in complex with LM10
ComponentsTryptophan 2,3-dioxygenase
KeywordsCYTOSOLIC PROTEIN / Human TDO / hTDO / LM10
Function / homology
Function and homology information


response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding ...response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / alpha-methyl-L-tryptophan / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsIshigami, I. / Yeh, S.-R. / Lewis-Ballester, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115773 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151419 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structural Insights into Protein-Inhibitor Interactions in Human Tryptophan Dioxygenase.
Authors: Geeraerts, Z. / Ishigami, I. / Lewis-Ballester, A. / Pham, K.N. / Kozlova, A. / Mathieu, C. / Frederick, R. / Yeh, S.R.
History
DepositionFeb 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 11, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Tryptophan 2,3-dioxygenase
BBB: Tryptophan 2,3-dioxygenase
CCC: Tryptophan 2,3-dioxygenase
DDD: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,75715
Polymers180,7304
Non-polymers4,02711
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27120 Å2
ΔGint-174 kcal/mol
Surface area55810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.428, 152.919, 87.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUAAAA39 - 38923 - 373
221LEULEUBBBB39 - 38923 - 373
312HISHISAAAA39 - 39123 - 375
422HISHISCCCC39 - 39123 - 375
513GLUGLUAAAA39 - 39023 - 374
623GLUGLUDDDD39 - 39023 - 374
714LEULEUBBBB39 - 38923 - 373
824LEULEUCCCC39 - 38923 - 373
915LEULEUBBBB39 - 38923 - 373
1025LEULEUDDDD39 - 38923 - 373
1116GLUGLUCCCC39 - 39023 - 374
1226GLUGLUDDDD39 - 39023 - 374

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Tryptophan 2,3-dioxygenase / TDO / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TRPO / Tryptophan pyrrolase / Tryptophanase


Mass: 45182.535 Da / Num. of mol.: 4 / Fragment: UNP residues 18-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDO2, TDO / Production host: Escherichia coli (E. coli) / References: UniProt: P48775, tryptophan 2,3-dioxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZIQ / alpha-methyl-L-tryptophan


Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1AER / 6-fluoro-3-[(E)-2-(1H-tetrazol-5-yl)ethenyl]-1H-indole


Mass: 229.213 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H8FN5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 50 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350

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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: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.29→52.31 Å / Num. obs: 85859 / % possible obs: 97.258 % / Redundancy: 6.6 % / Rpim(I) all: 0.076 / Net I/σ(I): 6.6
Reflection shellResolution: 2.29→2.41 Å / Rmerge(I) obs: 1.512 / Num. unique obs: 84922 / CC1/2: 0.139

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→30.002 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.192 / SU B: 10.066 / SU ML: 0.214 / Average fsc free: 0.8276 / Average fsc work: 0.8375 / Cross valid method: FREE R-VALUE / ESU R: 0.287 / ESU R Free: 0.216
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2381 4274 5.033 %
Rwork0.2023 80648 -
all0.204 --
obs-84922 97.258 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.428 Å2-0 Å2-0 Å2
2---0.136 Å20 Å2
3---0.564 Å2
Refinement stepCycle: LAST / Resolution: 2.29→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11483 0 287 189 11959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312074
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511403
X-RAY DIFFRACTIONr_angle_refined_deg1.761.68116314
X-RAY DIFFRACTIONr_angle_other_deg1.2981.59926145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80351344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36621.86726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.416152224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7281593
X-RAY DIFFRACTIONr_chiral_restr0.0750.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213431
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023044
X-RAY DIFFRACTIONr_nbd_refined0.2230.22600
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.210425
X-RAY DIFFRACTIONr_nbtor_refined0.1720.25723
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.25588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2490.217
X-RAY DIFFRACTIONr_nbd_other0.2950.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.20.28
X-RAY DIFFRACTIONr_mcbond_it5.6595.7965427
X-RAY DIFFRACTIONr_mcbond_other5.6565.7955423
X-RAY DIFFRACTIONr_mcangle_it8.4578.6686754
X-RAY DIFFRACTIONr_mcangle_other8.4598.676753
X-RAY DIFFRACTIONr_scbond_it5.7726.266647
X-RAY DIFFRACTIONr_scbond_other5.7716.266646
X-RAY DIFFRACTIONr_scangle_it8.7479.1719560
X-RAY DIFFRACTIONr_scangle_other8.7479.1729561
X-RAY DIFFRACTIONr_lrange_it11.51464.32513920
X-RAY DIFFRACTIONr_lrange_other11.5264.33713894
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.0511156
X-RAY DIFFRACTIONr_ncsr_local_group_20.090.0510594
X-RAY DIFFRACTIONr_ncsr_local_group_30.0930.0511092
X-RAY DIFFRACTIONr_ncsr_local_group_40.0960.0510553
X-RAY DIFFRACTIONr_ncsr_local_group_50.090.0511107
X-RAY DIFFRACTIONr_ncsr_local_group_60.0940.0510595
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.088070.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.088070.05008
23AAAX-RAY DIFFRACTIONLocal ncs0.089840.05008
24CCCX-RAY DIFFRACTIONLocal ncs0.089840.05008
35AAAX-RAY DIFFRACTIONLocal ncs0.093450.05008
36DDDX-RAY DIFFRACTIONLocal ncs0.093450.05008
47BBBX-RAY DIFFRACTIONLocal ncs0.095950.05008
48CCCX-RAY DIFFRACTIONLocal ncs0.095950.05008
59BBBX-RAY DIFFRACTIONLocal ncs0.08950.05008
510DDDX-RAY DIFFRACTIONLocal ncs0.08950.05008
611CCCX-RAY DIFFRACTIONLocal ncs0.094010.05008
612DDDX-RAY DIFFRACTIONLocal ncs0.094010.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.29-2.3490.3642650.36949480.36963530.4980.52382.05570.368
2.349-2.4130.3622840.36354410.36361680.570.56192.81780.361
2.413-2.4830.3522970.34555150.34560150.6520.65896.62510.344
2.483-2.5580.3382650.31954620.3258830.7250.72797.34830.316
2.558-2.6420.3542680.29452610.29756640.7840.80197.61650.287
2.642-2.7340.3072720.27951590.28155210.8160.82698.36990.266
2.734-2.8360.2982640.24249820.24553030.8630.88198.92510.227
2.836-2.9510.2812600.22548160.22751190.8810.90299.160.206
2.951-3.0810.2722690.2145950.21348990.8960.91399.28560.192
3.081-3.2290.2522390.20544790.20747320.9120.92499.70410.19
3.229-3.4020.2442310.19242520.19444950.9190.9499.7330.178
3.402-3.6050.2392260.19440350.19642690.930.94199.81260.184
3.605-3.850.2152020.17838170.1840200.9450.95899.97510.173
3.85-4.1530.1761810.14235860.14337670.9660.9731000.141
4.153-4.540.1621810.13632940.13734750.970.9711000.141
4.54-5.0620.1761530.14130010.14231540.9640.9711000.148
5.062-5.8180.1931250.16427140.16528390.9620.9691000.17
5.818-7.0590.2241240.18722850.18924090.9460.9591000.195
7.059-9.7170.1961080.15618410.15819500.9620.9799.94870.181
9.717-30.0020.25600.2311650.23112280.9460.95499.75570.267

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