[English] 日本語
Yorodumi
- PDB-6io0: Human IDH1 R132C mutant complexed with compound A. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6io0
TitleHuman IDH1 R132C mutant complexed with compound A.
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / ISO-CITRATE DEHYDROGENASE / ALLOSTERIC INHIBITOR / NADPH
Function / homology
Function and homology information


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / 2-oxoglutarate metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / 2-oxoglutarate metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / NAD binding / tertiary granule lumen / peroxisome / NADP binding / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AOU / CITRIC ACID / Chem-NDP / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSuzuki, M. / Baba, D. / Hanzawa, H.
CitationJournal: Mol.Cancer Ther. / Year: 2020
Title: A Potent Blood-Brain Barrier-Permeable Mutant IDH1 Inhibitor Suppresses the Growth of Glioblastoma with IDH1 Mutation in a Patient-Derived Orthotopic Xenograft Model.
Authors: Machida, Y. / Nakagawa, M. / Matsunaga, H. / Yamaguchi, M. / Ogawara, Y. / Shima, Y. / Yamagata, K. / Katsumoto, T. / Hattori, A. / Itoh, M. / Seki, T. / Nishiya, Y. / Nakamura, K. / Suzuki, ...Authors: Machida, Y. / Nakagawa, M. / Matsunaga, H. / Yamaguchi, M. / Ogawara, Y. / Shima, Y. / Yamagata, K. / Katsumoto, T. / Hattori, A. / Itoh, M. / Seki, T. / Nishiya, Y. / Nakamura, K. / Suzuki, K. / Imaoka, T. / Baba, D. / Suzuki, M. / Sampetrean, O. / Saya, H. / Ichimura, K. / Kitabayashi, I.
History
DepositionOct 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,01116
Polymers93,3322
Non-polymers3,67914
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-40 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.750, 82.750, 296.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Isocitrate dehydrogenase [NADP] cytoplasmic / Cytosolic NADP-isocitrate dehydrogenase / IDP / NADP(+)-specific ICDH


Mass: 46666.172 Da / Num. of mol.: 2 / Mutation: R132C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Production host: Escherichia coli (E. coli)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)

-
Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-AOU / (2E)-3-{3-[3-(2,6-dichlorophenyl)-5-(propan-2-yl)-1,2-oxazole-4-carbonyl]-1-methyl-1H-indol-7-yl}prop-2-enoic acid


Mass: 483.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H20Cl2N2O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5M ammonium citrate tribasic (pH 7.0), 2.5mM DTT. micro-seeding.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→79.7 Å / Num. obs: 50571 / % possible obs: 94.8 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.049 / Rrim(I) all: 0.093 / Net I/σ(I): 8.1 / Num. measured all: 174645 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.272.80.52529620.5580.3610.64166.3
9.07-79.730.0298970.9980.0190.03599

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.2data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.303 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.217 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 2526 5 %RANDOM
Rwork0.1895 ---
obs0.1928 47969 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.46 Å2 / Biso mean: 42.932 Å2 / Biso min: 20.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å2-0 Å2-0 Å2
2--0.94 Å2-0 Å2
3----1.89 Å2
Refinement stepCycle: final / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6170 0 243 249 6662
Biso mean--56.05 45.15 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126548
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.6528876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82623.624298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.769151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3441524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024924
LS refinement shellResolution: 2.2→2.277 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.342 173 -
Rwork0.302 3177 -
all-3350 -
obs--65.71 %

+
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