[English] 日本語
Yorodumi
- PDB-9etv: Holo IDO with a bound inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9etv
TitleHolo IDO with a bound inhibitor
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / heme
Function / homology
Function and homology information


ommochrome biosynthetic process / compound eye pigmentation / Tryptophan catabolism / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / kynurenine metabolic process / L-tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / L-tryptophan catabolic process / protein homotetramerization ...ommochrome biosynthetic process / compound eye pigmentation / Tryptophan catabolism / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / kynurenine metabolic process / L-tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / L-tryptophan catabolic process / protein homotetramerization / heme binding / metal ion binding
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 / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsWicki, M. / Mac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SAR and cellular potency optimization of novel heme-binding IDO1 inhibitors
Authors: Cren, S. / Lotz, C. / Mac Sweeney, A. / Lange, R. / Kimmerlin, T.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0533
Polymers43,3051
Non-polymers7492
Water181
1
A: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,21312
Polymers173,2194
Non-polymers2,9958
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_445-y-1,-x-1,-z+1/31
Buried area26760 Å2
ΔGint-188 kcal/mol
Surface area54200 Å2
Unit cell
Length a, b, c (Å)113.382, 113.382, 213.926
Angle α, β, γ (deg.)90, 90, 120
Int Tables number181
Space group name H-MP6422

-
Components

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


Mass: 43304.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: v, CG5163 / Production host: Escherichia coli (E. coli) / References: UniProt: P20351, tryptophan 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-A1H61 / 6-methylimidazo[1,5-a]pyridine


Mass: 132.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0M NaMalonate pH 5.0, 0.1M NaAcetate pH 4.50, 2% PEG 20,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.1 Å / Num. obs: 59933 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 1 / Rrim(I) all: 0.241 / Net I/σ(I): 9.81
Reflection shellResolution: 2.4→2.55 Å / Mean I/σ(I) obs: 0.59 / Num. unique obs: 9642 / CC1/2: 0.426 / Rrim(I) all: 5.36

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→49.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.207
RfactorNum. reflection% reflectionSelection details
Rfree0.2896 1622 -RANDOM
Rwork0.2597 ---
obs0.2612 32427 99.8 %-
Displacement parametersBiso mean: 86.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.7169 Å20 Å20 Å2
2---2.7169 Å20 Å2
3---5.4338 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 2.402→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 53 1 2889
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082954HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.843988HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes531HARMONIC5
X-RAY DIFFRACTIONt_it2954HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion363SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2331SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion19.07
LS refinement shellResolution: 2.402→2.42 Å
RfactorNum. reflection% reflection
Rfree0.6202 33 -
Rwork0.5899 --
obs--95.81 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more