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- PDB-9l6e: A novel allosteric covalent inhibitory site of fucosyltransferase... -

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Basic information

Entry
Database: PDB / ID: 9l6e
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
: / 4-HYDROXYPROLINE / 5-HYDROXYLYSINE / Alpha-(1,6)-fucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 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)116,62913
Polymers115,2782
Non-polymers1,35111
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-44 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.790, 67.910, 140.820
Angle α, β, γ (deg.)90.00, 132.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 13 molecules

#2: Chemical ChemComp-LYZ / 5-HYDROXYLYSINE


Type: L-peptide linking / Mass: 162.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O3
#3: Chemical
ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H9NO3
#4: Chemical ChemComp-A1EI1 / 2-ethynyl-4-[4-(5-oxidanylpentoxy)phenyl]benzaldehyde


Mass: 308.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging 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, 0.1 M MOPSO, 0. ...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, 0.1 M MOPSO, 0.1 M Bis-Tris pH 6.5, 15% w/v PEG 3000, 20% v/v 1, 2, 4-Butanetriol and 2% w/v NDSB 256.

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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: 3.07→71.46 Å / Num. obs: 25445 / % possible obs: 99.5 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.175 / Net I/σ(I): 8.6
Reflection shellResolution: 3.07→3.15 Å / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1846 / CC1/2: 0.744

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→71.46 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3105 1239 4.88 %
Rwork0.2287 --
obs0.2326 25404 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.07→71.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7245 0 91 2 7338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097517
X-RAY DIFFRACTIONf_angle_d1.15510174
X-RAY DIFFRACTIONf_dihedral_angle_d7.491006
X-RAY DIFFRACTIONf_chiral_restr0.0581084
X-RAY DIFFRACTIONf_plane_restr0.0141317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.190.34231650.28512650X-RAY DIFFRACTION100
3.19-3.340.38861250.27142655X-RAY DIFFRACTION99
3.34-3.510.33521310.25032690X-RAY DIFFRACTION99
3.51-3.730.36041370.23812638X-RAY DIFFRACTION99
3.73-4.020.33281490.22582673X-RAY DIFFRACTION100
4.02-4.430.281300.20422702X-RAY DIFFRACTION100
4.43-5.070.30951310.20082697X-RAY DIFFRACTION100
5.07-6.380.30181120.24382756X-RAY DIFFRACTION100
6.39-71.460.27271590.22172704X-RAY DIFFRACTION97

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