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

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Basic information

Entry
Database: PDB / ID: 8tic
TitleStructure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 1
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 / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / cellular response to leukemia inhibitory factor ...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 / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / cellular response to leukemia inhibitory factor / axon guidance / sensory perception of smell / Golgi membrane
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
Chem-FKX / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 19, 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 13, 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)189,80620
Polymers184,3444
Non-polymers5,46216
Water1,06359
1
A: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
C: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,99511
Polymers92,1722
Non-polymers2,8239
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint20 kcal/mol
Surface area30440 Å2
MethodPISA
2
B: 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)94,8119
Polymers92,1722
Non-polymers2,6397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint15 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.142, 92.394, 203.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 , 2 types, 6 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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: obtained synthetically / 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, 69 molecules

#4: Chemical
ChemComp-FKX / 3-(2-methylpropyl)-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxylic acid


Mass: 234.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.17 M sodium acetate, 0.08 M Tris pH 8.5, 25.5% PEG 4000, 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: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29.98 Å / Num. obs: 46965 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 44.13 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.392 / Rpim(I) all: 0.132 / Rrim(I) all: 0.415 / Net I/σ(I): 6.2
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 10 % / Rmerge(I) obs: 2.503 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4559 / CC1/2: 0.328 / Rpim(I) all: 0.822 / Rrim(I) all: 2.639 / % 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: 2.7→29.98 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 2004 4.27 %
Rwork0.2123 --
obs0.2145 46884 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10766 0 366 59 11191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411422
X-RAY DIFFRACTIONf_angle_d0.66515467
X-RAY DIFFRACTIONf_dihedral_angle_d11.4241644
X-RAY DIFFRACTIONf_chiral_restr0.0421706
X-RAY DIFFRACTIONf_plane_restr0.0041934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.39571440.33553123X-RAY DIFFRACTION100
2.77-2.840.34291430.29753159X-RAY DIFFRACTION100
2.84-2.930.30911390.27993175X-RAY DIFFRACTION100
2.93-3.020.31461350.27313161X-RAY DIFFRACTION100
3.02-3.130.33931410.25643172X-RAY DIFFRACTION100
3.13-3.250.30921420.26183167X-RAY DIFFRACTION100
3.25-3.40.2881440.23323193X-RAY DIFFRACTION100
3.4-3.580.31231450.20953194X-RAY DIFFRACTION100
3.58-3.80.25521480.21193159X-RAY DIFFRACTION100
3.8-4.10.22741360.1883237X-RAY DIFFRACTION100
4.1-4.510.21451410.16793206X-RAY DIFFRACTION100
4.51-5.160.21511500.16113244X-RAY DIFFRACTION100
5.16-6.490.24651440.19993276X-RAY DIFFRACTION100
6.49-29.980.23681520.18553414X-RAY DIFFRACTION100

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