[English] 日本語
Yorodumi
- PDB-5etw: Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5etw
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IDO1 / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / stereocilium bundle / tryptophan catabolic process to kynurenine / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / stereocilium bundle / tryptophan catabolic process to kynurenine / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / positive regulation of T cell apoptotic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / negative regulation of T cell proliferation / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-XNL / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsWu, S.Y. / Peng, Y.H. / Wu, J.S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1.
Authors: Peng, Y.H. / Ueng, S.H. / Tseng, C.T. / Hung, M.S. / Song, J.S. / Wu, J.S. / Liao, F.Y. / Fan, Y.S. / Wu, M.H. / Hsiao, W.C. / Hsueh, C.C. / Lin, S.Y. / Cheng, C.Y. / Tu, C.H. / Lee, L.C. / ...Authors: Peng, Y.H. / Ueng, S.H. / Tseng, C.T. / Hung, M.S. / Song, J.S. / Wu, J.S. / Liao, F.Y. / Fan, Y.S. / Wu, M.H. / Hsiao, W.C. / Hsueh, C.C. / Lin, S.Y. / Cheng, C.Y. / Tu, C.H. / Lee, L.C. / Cheng, M.F. / Shia, K.S. / Shih, C. / Wu, S.Y.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Indoleamine 2,3-dioxygenase 1
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5906
Polymers90,7682
Non-polymers1,8224
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-45 kcal/mol
Surface area30450 Å2
Unit cell
Length a, b, c (Å)85.674, 91.432, 128.373
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Indoleamine 2,3-dioxygenase 1 / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase


Mass: 45384.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-XNL / (1~{R})-1-cyclohexyl-2-pyrido[3,4-b]indol-9-yl-ethanol


Mass: 294.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG, Ammonium Fluoride / PH range: 5.5~7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 27758 / % possible obs: 97.6 % / Redundancy: 6 % / Biso Wilson estimate: 66.05 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Χ2: 1.054 / Net I/av σ(I): 24.783 / Net I/σ(I): 14.3 / Num. measured all: 165990
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.86.20.60927620.8560.2630.6651.04799.2
2.8-2.916.20.42527790.9230.1840.4641.03799.2
2.91-3.046.20.30827650.9530.1330.3361.08698.8
3.04-3.26.20.22327810.9730.0970.2431.05898.9
3.2-3.46.20.14727570.9890.0640.1611.07598.2
3.4-3.666.10.0927920.9950.0390.0981.03498.2
3.66-4.0360.05627670.9970.0250.0611.07698.1
4.03-4.615.60.04927630.9980.0220.0541.03996.7
4.61-5.85.70.04227800.9980.0190.0461.04496.4
5.8-305.40.03328120.9990.0150.0361.04292.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10_2152refinement
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t


Resolution: 2.7→28.74 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1403 5.06 %Random selection
Rwork0.1886 26313 --
obs0.19 27716 97.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.09 Å2 / Biso mean: 76.555 Å2 / Biso min: 36.98 Å2
Refinement stepCycle: final / Resolution: 2.7→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5856 0 130 106 6092
Biso mean--71.99 80.81 -
Num. residues----739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076143
X-RAY DIFFRACTIONf_angle_d0.6878343
X-RAY DIFFRACTIONf_chiral_restr0.041902
X-RAY DIFFRACTIONf_plane_restr0.0041052
X-RAY DIFFRACTIONf_dihedral_angle_d13.0222251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6973-2.79360.31021460.27642592273898
2.7936-2.90540.28311470.252632277999
2.9054-3.03750.27531390.242626276599
3.0375-3.19740.25981400.23842636277699
3.1974-3.39740.25561300.21592631276198
3.3974-3.65930.22661230.2012664278798
3.6593-4.02660.19661470.17182627277498
4.0266-4.60720.19291510.15852609276097
4.6072-5.79680.18991230.16942654277796
5.7968-28.74120.20011570.17562642279993
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)
14.48791.5832-2.04913.3393-1.37863.34130.1396-0.6276-0.22570.152-0.4359-0.6769-0.25891.1693-0.00120.7018-0.1472-0.00460.98990.06240.747842.197-1.0272-15.5577
24.94150.2336-1.71350.12620.19441.81540.16690.13150.6301-0.01620.05410.216-0.4266-0.08300.8003-0.1540.12340.6678-0.07060.701721.40573.6479-8.4811
30.98450.8756-0.5821.3745-1.73492.22970.14870.7923-0.3458-0.3514-0.14420.15340.1326-0.222300.8609-0.04130.10740.8193-0.07010.861325.4807-7.5522-22.8091
42.13420.80760.5361.407-0.3291.61620.2020.71470.4688-0.1977-0.17020.1651-0.2496-0.3654-0.00120.78980.02580.23530.77430.13460.73312.67240.8013-13.9265
52.727-0.3211-0.82182.35350.77921.6698-0.0759-0.6863-0.3210.21960.03650.7123-0.1791-1.368300.58840.08540.00740.8964-0.06910.763-6.9885-24.9096-23.0456
64.8751-0.54810.79152.7591-0.32883.4509-0.0064-0.1592-0.0708-0.1039-0.15590.2087-0.1057-0.8879-00.53930.0618-0.0410.5575-0.07870.5038-1.5627-25.9453-26.912
74.8531-0.94412.09361.3031-0.42841.10870.176-0.017-0.4872-0.1167-0.04080.04410.3164-0.0095-00.6670.03060.00820.4688-0.03790.54515.9746-35.8211-22.717
81.58220.73051.24150.45120.99851.85760.14110.42250.4836-0.5221-0.39360.0569-0.34750.134500.79160.1081-0.00390.54220.04570.79929.0323-16.5548-28.9251
90.1647-0.21910.17790.2063-0.19620.16370.4660.87581.5638-0.4728-0.3216-1.1651-0.51630.72730.00840.73440.0685-0.00820.74450.09640.900321.9354-20.2888-25.6733
103.2269-0.44790.64042.313-0.55511.90730.0960.63320.1389-0.1955-0.151-0.27650.07690.3971-00.59690.0978-0.02310.6275-0.00170.552525.8728-31.449-24.7879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 159 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 240 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 298 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 400 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 72 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 159 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 160 through 240 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 241 through 276 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 277 through 298 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 299 through 401 )B0

+
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