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- PDB-9l63: A novel allosteric covalent inhibitory site of fucosyltransferase... -

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Basic information

Entry
Database: PDB / ID: 9l63
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: 2.66 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)115,7373
Polymers115,2782
Non-polymers4601
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.430, 69.740, 141.690
Angle α, β, γ (deg.)90.00, 132.62, 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-A1EJM / 1-[(~{Z})-octadec-9-enoyl]oxy-2,5-bis(oxidanylidene)pyrrolidine-3-sulfonic acid


Mass: 459.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H37NO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.01M Spermine tetrahydrochloride, 0.01M Spermidine trihydrochloride, 0.01M 1,4-Diaminobutane dihydrochloride, 0.01M DL-Ornithine monohydrochloride, 0.01 M MOPSO, 0.1 M Bis-Tris pH 6.5, 10% ...Details: 0.01M Spermine tetrahydrochloride, 0.01M Spermidine trihydrochloride, 0.01M 1,4-Diaminobutane dihydrochloride, 0.01M DL-Ornithine monohydrochloride, 0.01 M MOPSO, 0.1 M Bis-Tris pH 6.5, 10% w/v PEG 8000 and 20% v/v 1,5-Pentanediol.

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Oct 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.66→32.24 Å / Num. obs: 40090 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.4
Reflection shellResolution: 2.66→2.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.943 / Num. unique obs: 2985 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→30.86 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 2074 5.18 %
Rwork0.2157 --
obs0.2186 40020 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7201 0 0 13 7214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097382
X-RAY DIFFRACTIONf_angle_d1.049989
X-RAY DIFFRACTIONf_dihedral_angle_d7.153984
X-RAY DIFFRACTIONf_chiral_restr0.0551064
X-RAY DIFFRACTIONf_plane_restr0.0111287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.720.37751370.35382532X-RAY DIFFRACTION100
2.72-2.790.38521230.33942562X-RAY DIFFRACTION100
2.79-2.870.37781240.31652507X-RAY DIFFRACTION100
2.87-2.950.38241270.30212542X-RAY DIFFRACTION100
2.95-3.040.34271280.29572529X-RAY DIFFRACTION99
3.04-3.150.37021420.29482520X-RAY DIFFRACTION100
3.15-3.280.33041650.27362489X-RAY DIFFRACTION100
3.28-3.430.32651240.25832557X-RAY DIFFRACTION100
3.43-3.610.2911530.24762485X-RAY DIFFRACTION100
3.61-3.830.25411360.22952540X-RAY DIFFRACTION100
3.83-4.130.28511310.21252551X-RAY DIFFRACTION100
4.13-4.540.24681530.18392505X-RAY DIFFRACTION100
4.54-5.20.24281360.17812549X-RAY DIFFRACTION99
5.2-6.540.24241550.20182539X-RAY DIFFRACTION99
6.54-30.860.21671400.15372539X-RAY DIFFRACTION96

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