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- PDB-6e37: O-GlcNAc Transferase in complex with covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 6.0E+37
TitleO-GlcNAc Transferase in complex with covalent inhibitor
Components
  • O-GlcNAc transferase subunit p110
  • TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
KeywordsTRANSFERASE/Inhibitor / O-GlcNAc Transferase / inhibitor / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Receptor Mediated Mitophagy / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / negative regulation of apoptotic signaling pathway / histone acetyltransferase complex / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / positive regulation of lipid biosynthetic process / mitophagy / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / negative regulation of cell migration / positive regulation of translation / Signal transduction by L1 / cell projection / response to insulin / Hsp90 protein binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / mitochondrial membrane / cellular response to glucose stimulus / protein processing / PML body / chromatin DNA binding / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / UCH proteinases / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / chromatin organization / HATs acetylate histones / positive regulation of cold-induced thermogenesis / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HQV / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.531 Å
AuthorsLi, H. / Jiang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121718 United States
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Targeted covalent inhibition of O-GlcNAc transferase in cells.
Authors: Worth, M. / Hu, C.W. / Li, H. / Fan, D. / Estevez, A. / Zhu, D. / Wang, A. / Jiang, J.
History
DepositionJul 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-GlcNAc transferase subunit p110
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0233
Polymers82,3732
Non-polymers6491
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area27500 Å2
MethodPISA
2
A: O-GlcNAc transferase subunit p110
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
hetero molecules

A: O-GlcNAc transferase subunit p110
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0456
Polymers164,7464
Non-polymers1,2992
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
Buried area6910 Å2
ΔGint-27 kcal/mol
Surface area50570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.656, 150.984, 198.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1230-

HOH

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Components

#1: Protein O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit / OGUDP-N-acetylglucosamine--peptide N- ...O-linked N-acetylglucosamine transferase 110 kDa subunit / OGUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunitT


Mass: 80974.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli (E. coli) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN


Mass: 1398.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68400*PLUS
#3: Chemical ChemComp-HQV / (2S,3R,4R,5S,6R)-3-[(2E)-but-2-enoylamino]-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 649.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H29N3O16P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.45 M potassium phosphate dibasic 10 mM EDTA 1% xylitol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 34188 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.992 / Net I/σ(I): 16
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1313 / CC1/2: 0.932 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3161: ???)refinement
HKL-20002.3.8data scaling
HKL-20002.3.8data scaling
Cootmodel building
RefinementResolution: 2.531→41.525 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1705 4.99 %
Rwork0.1671 --
obs0.1693 34179 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.531→41.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 41 191 5780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085741
X-RAY DIFFRACTIONf_angle_d0.9687801
X-RAY DIFFRACTIONf_dihedral_angle_d14.2823471
X-RAY DIFFRACTIONf_chiral_restr0.053864
X-RAY DIFFRACTIONf_plane_restr0.0061013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5312-2.60570.25021200.21662458X-RAY DIFFRACTION90
2.6057-2.68980.27251600.20042720X-RAY DIFFRACTION100
2.6898-2.78590.27791400.20062641X-RAY DIFFRACTION99
2.7859-2.89740.2411520.19482705X-RAY DIFFRACTION100
2.8974-3.02920.26561340.18452731X-RAY DIFFRACTION100
3.0292-3.18890.24951540.18782722X-RAY DIFFRACTION100
3.1889-3.38860.24581240.17252734X-RAY DIFFRACTION100
3.3886-3.65010.21761490.16042731X-RAY DIFFRACTION100
3.6501-4.01710.19651490.13932720X-RAY DIFFRACTION100
4.0171-4.59780.1541450.12682734X-RAY DIFFRACTION100
4.5978-5.79020.16551370.14792755X-RAY DIFFRACTION99
5.7902-41.53060.20931410.19212823X-RAY DIFFRACTION98

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