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- PDB-8tjc: Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 wit... -

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Basic information

Entry
Database: PDB / ID: 8tjc
TitleStructure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 8a
ComponentsN-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
KeywordsTRANSFERASE / acetylglucosaminyltransferase / inhibitor
Function / homology
Function and homology information


N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / keratan sulfate proteoglycan biosynthetic process / poly-N-acetyllactosamine biosynthetic process / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / Keratan sulfate biosynthesis / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / axon guidance ...N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / keratan sulfate proteoglycan biosynthetic process / poly-N-acetyllactosamine biosynthetic process / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / Keratan sulfate biosynthesis / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / axon guidance / cellular response to leukemia inhibitory factor / sensory perception of smell / Golgi membrane
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
Chem-HI8 / : / DI(HYDROXYETHYL)ETHER / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSudom, A. / Min, X.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Imidazolone as an Amide Bioisostere in the Development of beta-1,3- N -Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors.
Authors: Jackson, J.J. / Siegmund, A.C. / Bai, W.J. / Reed, A.B. / Birkholz, A.B. / Campuzano, I.D.G. / Crequer-Grandhomme, A. / Hu, R. / Modak, R.V. / Sudom, A. / Javier, N. / Sanders, C. / Lo, M.C. ...Authors: Jackson, J.J. / Siegmund, A.C. / Bai, W.J. / Reed, A.B. / Birkholz, A.B. / Campuzano, I.D.G. / Crequer-Grandhomme, A. / Hu, R. / Modak, R.V. / Sudom, A. / Javier, N. / Sanders, C. / Lo, M.C. / Xie, F. / Cee, V.J. / Manzanillo, P. / Allen, J.G.
History
DepositionJul 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
B: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
C: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
D: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,30522
Polymers184,3444
Non-polymers5,96218
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.410, 93.876, 205.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 / Beta-1 / 3-N-acetylglucosaminyltransferase 1 / BGnT-1 / 3-Gn-T1 / Beta3Gn-T1 / 3- ...Beta-1 / 3-N-acetylglucosaminyltransferase 1 / BGnT-1 / 3-Gn-T1 / Beta3Gn-T1 / 3-galactosyltransferase 7 / 3-GalTase 7 / Beta3Gal-T7 / Beta3GalT7 / b3Gal-T7 / Beta-3-Gx-T7 / UDP-Gal:beta-GlcNAc beta-1 / UDP-GlcNAc:betaGal beta-1 / 3-N-acetylglucosaminyltransferase 2 / BGnT-2 / 3-Gn-T2 / Beta3Gn-T2 / UDP-galactose:beta-N-acetylglucosamine beta-1


Mass: 46085.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B3GNT2, B3GALT7, B3GNT1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NY97, N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase

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Sugars , 6 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 134 molecules

#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mn
#8: Chemical
ChemComp-HI8 / (6M)-1-[(2R)-3,3-dimethylbutan-2-yl]-6-[(5S)-5-methyl-4-oxo-5-phenyl-4,5-dihydro-1H-imidazol-2-yl]-1,3-dihydro-2H-benzimidazol-2-one


Mass: 390.478 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C23H26N4O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1 M Tris 8.8, 0.16 M Sodium acetate, 25% PEG4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.01 Å / Num. obs: 88402 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 50.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.046 / Rrim(I) all: 0.168 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4513 / CC1/2: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JHK

7jhk


Resolution: 2.2→47.01 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 4351 4.93 %
Rwork0.2271 --
obs0.2295 88263 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10839 0 397 123 11359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211548
X-RAY DIFFRACTIONf_angle_d0.58815655
X-RAY DIFFRACTIONf_dihedral_angle_d6.071530
X-RAY DIFFRACTIONf_chiral_restr0.0421694
X-RAY DIFFRACTIONf_plane_restr0.0041991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.44751340.40172765X-RAY DIFFRACTION100
2.23-2.250.4631380.40892780X-RAY DIFFRACTION100
2.25-2.280.42341430.38392776X-RAY DIFFRACTION100
2.28-2.310.4181310.36892757X-RAY DIFFRACTION100
2.31-2.340.36521400.35242764X-RAY DIFFRACTION100
2.34-2.370.35681500.35582736X-RAY DIFFRACTION100
2.37-2.40.42391450.34852804X-RAY DIFFRACTION100
2.4-2.440.43921550.3612708X-RAY DIFFRACTION100
2.44-2.480.43821330.34532805X-RAY DIFFRACTION100
2.48-2.520.38381340.32322752X-RAY DIFFRACTION100
2.52-2.560.38931400.30872807X-RAY DIFFRACTION100
2.56-2.610.35021590.29412758X-RAY DIFFRACTION100
2.61-2.660.35241590.29472754X-RAY DIFFRACTION100
2.66-2.710.33191470.27362771X-RAY DIFFRACTION100
2.71-2.770.34061280.26742780X-RAY DIFFRACTION100
2.77-2.840.32961400.25882799X-RAY DIFFRACTION100
2.84-2.910.28811310.27822772X-RAY DIFFRACTION100
2.91-2.990.34381690.28922776X-RAY DIFFRACTION100
2.99-3.070.34431490.2762795X-RAY DIFFRACTION100
3.07-3.170.28721200.25732806X-RAY DIFFRACTION100
3.17-3.290.29311370.24972796X-RAY DIFFRACTION100
3.29-3.420.2851450.22572826X-RAY DIFFRACTION100
3.42-3.570.26571470.21932790X-RAY DIFFRACTION100
3.57-3.760.2571600.21412790X-RAY DIFFRACTION100
3.76-40.25831690.19532806X-RAY DIFFRACTION100
4-4.310.23211360.17722846X-RAY DIFFRACTION100
4.31-4.740.21151460.16512839X-RAY DIFFRACTION100
4.74-5.420.21341550.16992852X-RAY DIFFRACTION100
5.42-6.830.22741620.1982891X-RAY DIFFRACTION100
6.83-47.010.23151490.18173011X-RAY DIFFRACTION99

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