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- PDB-9l65: A novel allosteric covalent inhibitory site of fucosyltransferase... -

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Basic information

Entry
Database: PDB / ID: 9l65
TitleA novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures
ComponentsAlpha-(1,6)-fucosyltransferase
KeywordsTRANSFERASE / Inhibitors / Complex / Allosteric
Function / homology
Function and homology information


glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / : / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / L-fucose catabolic process / N-glycan processing ...glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / : / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / L-fucose catabolic process / N-glycan processing / regulation of cellular response to oxidative stress / : / respiratory gaseous exchange by respiratory system / fibroblast migration / protein N-linked glycosylation / Golgi cisterna membrane / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / SH3 domain binding / regulation of gene expression / Maturation of spike protein / in utero embryonic development / viral protein processing / Golgi membrane / Golgi apparatus / extracellular exosome / membrane
Similarity search - Function
Alpha-(1,6)-fucosyltransferase / Alpha-(1,6)-fucosyltransferase, SH3 domain / Alpha-(1,6)-fucosyltransferase, N- and catalytic domain / Alpha-(1,6)-fucosyltransferase N- and catalytic domains / Glycosyltransferase family 23 (GT23) domain / Glycosyltransferase family 23 (GT23) domain profile. / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
: / Alpha-(1,6)-fucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsJiang, J. / Fang, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures
Authors: Jiang, J. / Fang, P.
History
DepositionDec 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-(1,6)-fucosyltransferase
B: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2314
Polymers115,2782
Non-polymers9532
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-29 kcal/mol
Surface area38400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.360, 69.220, 105.120
Angle α, β, γ (deg.)90.00, 118.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-(1,6)-fucosyltransferase / Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6- ...Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6-fucosyltransferase / GDP-fucose--glycoprotein fucosyltransferase / Glycoprotein 6-alpha-L-fucosyltransferase


Mass: 57638.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUT8 / Production host: Homo sapiens (human)
References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase
#2: Chemical ChemComp-A1EJN / [2,6-bis(oxidanylidene)piperidin-1-yl] 18-(2,3-dimethylimidazol-1-ium-1-yl)octadecanoate


Mass: 476.672 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.02M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L-proline, 0.1M BES, 0.1 ...Details: 0.02M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L-proline, 0.1M BES, 0.1 M Triethanolamine (TEA) pH 7.5, 12.5% w/v PEG 4000 and 20% w/v 1,2,6-Hexanetriol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.97→92.19 Å / Num. obs: 86592 / % possible obs: 98.9 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.024 / Rrim(I) all: 0.059 / Χ2: 0.95 / Net I/σ(I): 19.5 / Num. measured all: 503443
Reflection shellResolution: 1.97→2.02 Å / % possible obs: 93.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.345 / Num. measured all: 23795 / Num. unique obs: 5963 / CC1/2: 0.903 / Rpim(I) all: 0.196 / Rrim(I) all: 0.4 / Χ2: 0.73 / Net I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→52.46 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 4179 4.96 %
Rwork0.1776 --
obs0.1792 84231 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→52.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 52 781 8048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087421
X-RAY DIFFRACTIONf_angle_d0.94510036
X-RAY DIFFRACTIONf_dihedral_angle_d6.9231014
X-RAY DIFFRACTIONf_chiral_restr0.0571065
X-RAY DIFFRACTIONf_plane_restr0.0091294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.2761470.22492484X-RAY DIFFRACTION94
2.01-2.040.22851280.20932627X-RAY DIFFRACTION97
2.04-2.060.24471510.19662621X-RAY DIFFRACTION99
2.06-2.090.25971300.19792665X-RAY DIFFRACTION99
2.09-2.110.21781480.19222593X-RAY DIFFRACTION98
2.11-2.140.23971280.18552678X-RAY DIFFRACTION99
2.14-2.170.20541330.18812652X-RAY DIFFRACTION98
2.17-2.210.25481350.18292654X-RAY DIFFRACTION100
2.21-2.240.23081390.18812665X-RAY DIFFRACTION99
2.24-2.280.21971300.18232669X-RAY DIFFRACTION100
2.28-2.320.25211300.18522688X-RAY DIFFRACTION99
2.32-2.360.2531390.18712647X-RAY DIFFRACTION100
2.36-2.40.22361440.19192693X-RAY DIFFRACTION100
2.4-2.450.22131350.19252638X-RAY DIFFRACTION100
2.45-2.510.25861580.18952672X-RAY DIFFRACTION99
2.51-2.570.22781350.19022696X-RAY DIFFRACTION100
2.57-2.630.23051540.19432665X-RAY DIFFRACTION100
2.63-2.70.26441370.19622676X-RAY DIFFRACTION99
2.7-2.780.26591480.19882665X-RAY DIFFRACTION100
2.78-2.870.2441330.19762725X-RAY DIFFRACTION100
2.87-2.970.2086970.19582718X-RAY DIFFRACTION100
2.97-3.090.20371430.18392668X-RAY DIFFRACTION100
3.09-3.230.20981510.19442694X-RAY DIFFRACTION99
3.23-3.40.20531220.18462709X-RAY DIFFRACTION100
3.4-3.620.21911430.17332693X-RAY DIFFRACTION100
3.62-3.890.2031250.16762701X-RAY DIFFRACTION99
3.89-4.290.15991560.15192673X-RAY DIFFRACTION100
4.29-4.910.18241580.14072706X-RAY DIFFRACTION99
4.91-6.180.16961640.16622702X-RAY DIFFRACTION99
6.18-52.460.17871380.15792715X-RAY DIFFRACTION96

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