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- PDB-7lu7: Human TDO (hTDO) in complex with NLG919 analog -

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Basic information

Entry
Database: PDB / ID: 7lu7
TitleHuman TDO (hTDO) in complex with NLG919 analog
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / human TDO / human TDO2 / hTDO / hTDO2 / NLG919
Function / homology
Function and homology information


response to nitroglycerin / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding ...response to nitroglycerin / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
Chem-5PK / 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: 2.3 Å
AuthorsYeh, S.-R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115773 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 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)185,19916
Polymers180,7304
Non-polymers4,46812
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25860 Å2
ΔGint-176 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.263, 153.811, 87.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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
#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
#4: Chemical
ChemComp-5PK / (1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol


Mass: 282.380 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H22N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 293 K / Method: microbatch
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: 0.979 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 5, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.299→29.968 Å / Num. obs: 86779 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.998 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.7 % / Num. unique obs: 4507 / CC1/2: 0.999 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6PYZ

6pyz


Resolution: 2.3→29.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.554 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.212
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2364 4304 4.96 %
Rwork0.1894 82475 -
all0.192 --
obs-86779 99.604 %
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: 50.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.299 Å2-0 Å20 Å2
2---1.115 Å20 Å2
3---1.415 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11364 0 320 397 12081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311996
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711376
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.66916202
X-RAY DIFFRACTIONr_angle_other_deg1.2671.59126096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4151329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56121.917720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.514152213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.341592
X-RAY DIFFRACTIONr_chiral_restr0.0730.21409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213286
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023018
X-RAY DIFFRACTIONr_nbd_refined0.2070.22523
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.210319
X-RAY DIFFRACTIONr_nbtor_refined0.170.25689
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2396
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.213
X-RAY DIFFRACTIONr_nbd_other0.1930.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.29
X-RAY DIFFRACTIONr_mcbond_it4.0815.155352
X-RAY DIFFRACTIONr_mcbond_other4.0725.155351
X-RAY DIFFRACTIONr_mcangle_it6.2287.6986669
X-RAY DIFFRACTIONr_mcangle_other6.2297.6996670
X-RAY DIFFRACTIONr_scbond_it4.2335.5816644
X-RAY DIFFRACTIONr_scbond_other4.2335.5816645
X-RAY DIFFRACTIONr_scangle_it6.6928.1789533
X-RAY DIFFRACTIONr_scangle_other6.6928.1789534
X-RAY DIFFRACTIONr_lrange_it10.83794.23548678
X-RAY DIFFRACTIONr_lrange_other10.84194.28348485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.3590.3172950.2835975X-RAY DIFFRACTION98.6314
2.359-2.4230.2932960.2645846X-RAY DIFFRACTION99.1765
2.423-2.4930.3113100.2615703X-RAY DIFFRACTION99.4377
2.493-2.570.2713200.2325522X-RAY DIFFRACTION99.6418
2.57-2.6540.2742940.2185417X-RAY DIFFRACTION99.7903
2.654-2.7480.252640.2065210X-RAY DIFFRACTION99.7631
2.748-2.8510.2272460.1925115X-RAY DIFFRACTION100
2.851-2.9680.2662420.1964835X-RAY DIFFRACTION99.9409
2.968-3.10.282440.1934679X-RAY DIFFRACTION99.9797
3.1-3.2510.2452460.1944499X-RAY DIFFRACTION99.9579
3.251-3.4270.2442300.1894255X-RAY DIFFRACTION99.9777
3.427-3.6340.2542360.194005X-RAY DIFFRACTION100
3.634-3.8850.2291940.1753828X-RAY DIFFRACTION100
3.885-4.1960.1942020.1593561X-RAY DIFFRACTION100
4.196-4.5960.2111430.1463303X-RAY DIFFRACTION100
4.596-5.1380.1991650.1512995X-RAY DIFFRACTION100
5.138-5.9320.2571350.2092661X-RAY DIFFRACTION100
5.932-7.2620.2241100.1812287X-RAY DIFFRACTION100
7.262-10.2590.159830.1381794X-RAY DIFFRACTION99.5228
10.259-29.950.188490.225985X-RAY DIFFRACTION92.9021

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