9L6E | pdb_00009l6e

A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures

PDB DOI: https://doi.org/10.2210/pdb9L6E/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-12-24 Released: 2026-01-07
Deposition Author(s): Jiang, J., Fang, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free:
0.310 (Depositor), 0.306 (DCC)
R-Value Work:
0.229 (Depositor), 0.249 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures

Jiang, J., Fang, P.

To be published.

Macromolecule Content

Total Structure Weight: 116.63 kDa
Atom Count: 7,338
Modeled Residue Count: 889
Deposited Residue Count: 998
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-(1,6)-fucosyltransferase	A, B	499	Homo sapiens	Mutation(s): 0 Gene Names: FUT8 EC: 2.4.1.68
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYC5 (Homo sapiens) Explore Q9BYC5 Go to UniProtKB: Q9BYC5
PHAROS: Q9BYC5 GTEx: ENSG00000033170
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EI1 (Subject of Investigation/LOI) Query on A1EI1 Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	2-ethynyl-4-[4-(5-oxidanylpentoxy)phenyl]benzaldehyde C₂₀ H₂₀ O₃ JVRBFNAJZRWUKE-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
LYZ Query on LYZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5-HYDROXYLYSINE C₆ H₁₄ N₂ O₃ YSMODUONRAFBET-UHNVWZDZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
HYP Query on HYP Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] G [auth B] H [auth B] I [auth B] D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	4-HYDROXYPROLINE C₅ H₉ N O₃ PMMYEEVYMWASQN-DMTCNVIQSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]