6Z6Y: Galectin-8 N-terminal domain

Galectin-8 N-terminal domain in complex with a sulfatide mimicking a sphingolipid. Determined by X-ray diffraction at 1.34 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 1.34 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,436
Mol. weight: 18.53 kDa
Ligands: L4L
Released: 30 Dec 2020

Explore 6Z6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z6Y contains 3 α-helices and 13 β-strands across 1 chain. 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	9-13	5	1
β-strand	19-22	4	2
β-strand	31-38	8	1
β-strand	45-56	12	2
β-strand	59-69	11	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	145-153	9	1
α-helix	157-159	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Galectin-8	A	protein	156	Homo sapiens	O00214 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Z6Y_1 Galectin-8 (chains A)
LNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAF
HFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTL
LYGHRIGPEKIDTLGIYGKVNIHSIGFSFSSDLQST

Ligands and cofactors

ID	Name	Formula	Copies
L4L	[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S})-2-acetamido-3-oxidanylidene-pent-4-…	C13 H21 N O11 S	1

Water and common crystallization additives (ACT, PGE) are not listed.

Primary citation

Probing sulfatide-tissue lectin recognition with functionalized glycodendrimersomes. Murphy, P.V., Romero, A., Xiao, Q. et al. iScience (2021) 24:101919-101919. DOI 10.1016/j.isci.2020.101919 · 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
9FYJ 1.08 Å, N-terminal domain of human galectin-8 in complex with an alpha-galactoside ligand
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…
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…

Browse structure collections

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