[English] 日本語
Yorodumi
- PDB-9uz2: Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9uz2
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with Cyanide ion
ComponentsMaltose/maltodextrin-binding periplasmic protein,Indoleamine 2,3-dioxygenase 2
KeywordsOXIDOREDUCTASE / HEM protein / Complex
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / indoleamine 2,3-dioxygenase activity / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / : / Tryptophan catabolism / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport ...Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / indoleamine 2,3-dioxygenase activity / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / : / Tryptophan catabolism / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / immune system process / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / heme binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / CITRIC ACID / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Maltose/maltodextrin-binding periplasmic protein / Indoleamine 2,3-dioxygenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTakahashi, A. / Inoue, T. / Fukuda, Y. / Adachi, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Febs J. / Year: 2026
Title: Human IDO2 exhibits unique binding affinities distinct to those of human IDO1.
Authors: Nogi, S. / Takahashi, A. / Murakami, S. / Adachi, N. / Fujimoto, T. / Fukuda, Y. / Yamashita, T. / Inoue, T. / Tsujino, H.
History
DepositionMay 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Indoleamine 2,3-dioxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1508
Polymers86,8261
Non-polymers1,3247
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-22 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.505, 197.505, 93.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Indoleamine 2,3-dioxygenase 2 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IDO-2 / Indoleamine 2 / 3- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IDO-2 / Indoleamine 2 / 3-dioxygenase-like protein 1 / Indoleamine-pyrrole 2


Mass: 86825.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: malE, Z5632, ECs5017, IDO2, INDOL1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEY0, UniProt: Q6ZQW0, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 6 types, 161 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.07 Å3/Da / Density % sol: 79.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium citrate tribasic dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→49.38 Å / Num. obs: 98295 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.121 / Net I/σ(I): 10.9
Reflection shellResolution: 2.55→2.61 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9707 / CC1/2: 0.568

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→48.7 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 3343 4.88 %
Rwork0.2051 --
obs0.2067 68473 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5805 0 90 155 6050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116063
X-RAY DIFFRACTIONf_angle_d1.3068247
X-RAY DIFFRACTIONf_dihedral_angle_d11.802821
X-RAY DIFFRACTIONf_chiral_restr0.064905
X-RAY DIFFRACTIONf_plane_restr0.0091057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.590.42581510.42622665X-RAY DIFFRACTION100
2.59-2.630.39321400.39912686X-RAY DIFFRACTION100
2.63-2.670.35741120.37152764X-RAY DIFFRACTION100
2.67-2.710.38161510.36072646X-RAY DIFFRACTION100
2.71-2.760.35041120.35282700X-RAY DIFFRACTION100
2.76-2.810.43211420.34292692X-RAY DIFFRACTION100
2.81-2.860.34991500.33082708X-RAY DIFFRACTION100
2.86-2.920.33511230.31732705X-RAY DIFFRACTION100
2.92-2.980.32391480.30772691X-RAY DIFFRACTION100
2.98-3.050.34641260.31772692X-RAY DIFFRACTION100
3.05-3.130.41530.30982704X-RAY DIFFRACTION100
3.13-3.210.31721240.27512705X-RAY DIFFRACTION100
3.21-3.310.28861580.25072677X-RAY DIFFRACTION100
3.31-3.410.27941400.22892718X-RAY DIFFRACTION100
3.41-3.540.26461600.22932698X-RAY DIFFRACTION100
3.54-3.680.28451010.21372728X-RAY DIFFRACTION100
3.68-3.840.22091350.19352713X-RAY DIFFRACTION100
3.84-4.050.20741480.16682723X-RAY DIFFRACTION100
4.05-4.30.20761320.15542729X-RAY DIFFRACTION100
4.3-4.630.21491620.14472697X-RAY DIFFRACTION100
4.63-5.10.14231510.15492721X-RAY DIFFRACTION100
5.1-5.830.20651360.17692766X-RAY DIFFRACTION100
5.84-7.340.23251310.18032774X-RAY DIFFRACTION100
7.35-48.70.18241570.16252828X-RAY DIFFRACTION99

+
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