9FYJ: N-terminal domain of human galectin-8

N-terminal domain of human galectin-8 in complex with an alpha-galactoside ligand. Determined by X-ray diffraction at 1.08 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 1.08 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,894
Mol. weight: 35.73 kDa
Ligands: A1IHE
Released: 12 Mar 2025

Explore 9FYJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FYJ contains 3 α-helices and 26 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	19-22	4	2
β-strand	32-38	7	1
β-strand	45-52	8	2
α-helix	60	1
β-strand	61-69	9	2
β-strand	75-82	8	2
β-strand	85-86	2	2
β-strand	90-92	3	2
β-strand	102-109	8	1
β-strand	113-118	6	1
β-strand	121-127	7	1
α-helix	132-134	3
β-strand	137-142	6	2
β-strand	145-152	8	1

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	3
β-strand	19-22	4	4
β-strand	32-38	7	3
β-strand	45-56	12	4
β-strand	59-69	11	4
β-strand	75-82	8	4
β-strand	85-86	2	4
β-strand	90-92	3	4
β-strand	102-109	8	3
β-strand	113-118	6	3
β-strand	121-127	7	3
α-helix	132-134	3
β-strand	137-142	6	4
β-strand	145-152	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 1 of Galectin-8	A, B	protein	153	Homo sapiens	O00214 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9FYJ_1 Isoform 1 of Galectin-8 (chains A, B)
SLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVA
FHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHT
LLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSSD

Ligands and cofactors

ID	Name	Formula	Copies
A1IHE	2-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxyme…	C25 H24 Cl2 N2 O7 S	2

Water and common crystallization additives (CL) are not listed.

Primary citation

Nanomolar inhibitor of the galectin-8 N-terminal domain binds via a non-canonical cation-pi interaction. Puric, E., Hassan, M., Sjovall, F. et al. Commun Chem (2025) 8:59-59. DOI 10.1038/s42004-025-01458-6 · PubMed

Other PDB entries of the same protein (UniProt O00214 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GZC 1.08 Å, Crystal structure of Galectin-8 N-CRD with part of linker
5GZD 1.19 Å, Galectin-8 N-terminal domain carbohydrate recognition domain
9FXZ 1.3 Å, Galectin-8 N-terminal carbohydrate recognition domain in complex with…
5GZE 1.32 Å, Galectin-8 N-terminal domain carbohydrate recognition domain
3AP9 1.33 Å, Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in…
6Z6Y 1.34 Å, Galectin-8 N-terminal domain in complex with a sulfatide mimicking a sphingolipid
7ALS 1.35 Å, Alpha and beta Lactose isomer structure of Galectin 8, N-terminal domain
4BMB 1.35 Å, Crystal structure of the N terminal domain of human Galectin 8
31ML 1.5 Å, Crystal structure of the complex of galectin-8N-Methyl 2,6-anhydro-3-deoxy-3-S-(b-D-galac…
7P1M 1.52 Å, Galectin-8 N-terminal carbohydrate recognition domain in complex with benzimidazole…
3AP7 1.53 Å, Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in…
3AP6 1.58 Å, Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in…

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