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- PDB-9l64: A novel allosteric covalent inhibitory site of fucosyltransferase... -

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Basic information

Entry
Database: PDB / ID: 9l64
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: 2.49 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)116,0734
Polymers115,2782
Non-polymers7952
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-32 kcal/mol
Surface area38520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.514, 70.242, 105.606
Angle α, β, γ (deg.)90.00, 118.61, 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-A1EI0 / 1-hexadecyl-2-methyl-3-(phenylmethyl)imidazol-3-ium


Mass: 397.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H45N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.001M Rubidium chloride, 0.001M Strontium acetate, 0.001M Cesium acetate, 0.001M Barium acetate, 0.1 M MOPSO, 0.1 M Bis-Tris pH 6.5, 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: BL02U1 / Wavelength: 0.97918 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Jun 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.49→86.26 Å / Num. obs: 43902 / % possible obs: 98.7 % / Redundancy: 4.3 % / CC1/2: 0.982 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.058 / Rrim(I) all: 0.124 / Χ2: 0.92 / Net I/σ(I): 10.5 / Num. measured all: 188104
Reflection shellResolution: 2.49→2.63 Å / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.56 / Num. measured all: 21584 / Num. unique obs: 6420 / CC1/2: 0.778 / Rpim(I) all: 0.344 / Rrim(I) all: 0.661 / Χ2: 0.78 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→51.95 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 2180 4.97 %
Rwork0.1844 --
obs0.1869 43879 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→51.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7189 0 58 262 7509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087421
X-RAY DIFFRACTIONf_angle_d0.95110037
X-RAY DIFFRACTIONf_dihedral_angle_d6.8151025
X-RAY DIFFRACTIONf_chiral_restr0.051066
X-RAY DIFFRACTIONf_plane_restr0.0091298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.30231260.23822608X-RAY DIFFRACTION99
2.55-2.60.30341600.23122582X-RAY DIFFRACTION100
2.6-2.670.29081290.23872414X-RAY DIFFRACTION96
2.67-2.740.3161150.23722382X-RAY DIFFRACTION96
2.74-2.820.29761440.22652649X-RAY DIFFRACTION100
2.82-2.910.28221270.2122616X-RAY DIFFRACTION100
2.91-3.020.27721410.20722603X-RAY DIFFRACTION100
3.02-3.140.25441470.19922646X-RAY DIFFRACTION100
3.14-3.280.24851140.20762636X-RAY DIFFRACTION100
3.28-3.450.23771530.1942619X-RAY DIFFRACTION100
3.45-3.670.2281610.1842611X-RAY DIFFRACTION100
3.67-3.950.22331190.17772665X-RAY DIFFRACTION100
3.95-4.350.22971160.16072676X-RAY DIFFRACTION100
4.35-4.980.1881460.14692646X-RAY DIFFRACTION100
4.98-6.270.21071170.16872669X-RAY DIFFRACTION99
6.27-51.950.19231650.16162677X-RAY DIFFRACTION98

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