5GLZ: Tl-gal with Glucose

Tl-gal with Glucose. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Toxascaris leonina
Chains: 4
Atoms: 9,649
Mol. weight: 130.02 kDa
Ligands: BGC
Released: 9 Nov 2016

Explore 5GLZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GLZ contains 8 α-helices and 104 β-strands across 4 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: 1 helix, 27 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
β-strand	11-14	4	2
β-strand	24-30	7	1
β-strand	37-43	7	2
β-strand	54-61	8	2
β-strand	66-73	8	2
β-strand	76-77	2	2
β-strand	81-84	4	2
β-strand	92-99	8	1
β-strand	103-108	6	1
β-strand	111-117	7	1
α-helix	122-124	3
β-strand	127-132	6	2
β-strand	135-142	8	1
β-strand	146	1	3
β-strand	150-153	4	4
β-strand	159	1	4
β-strand	164-171	8	3
β-strand	177-184	8	4
β-strand	189-196	8	4
β-strand	201-208	8	4
β-strand	211-212	2	4
β-strand	216	1	4
β-strand	229-235	7	3
β-strand	239-244	6	3
β-strand	247-253	7	3
β-strand	261-268	8	4
β-strand	270-277	8	3

Chain B: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	8	1
β-strand	11-14	4	5
β-strand	24-30	7	6
β-strand	37-43	7	5
β-strand	54-61	8	5
β-strand	66-73	8	5
β-strand	76-77	2	5
β-strand	81-84	4	5
β-strand	93-99	7	6
β-strand	103-108	6	6
β-strand	111-117	7	6
α-helix	122-124	3
β-strand	127-132	6	5
β-strand	135-142	8	6
β-strand	146	1	7
β-strand	150-153	4	8
β-strand	163-171	9	7
β-strand	177-184	8	8
β-strand	189-196	8	8
β-strand	201-208	8	8
β-strand	211-212	2	8
β-strand	216	1	8
β-strand	229-235	7	7
β-strand	239-244	6	7
β-strand	247-253	7	7
β-strand	261-268	8	8
β-strand	270-277	8	7

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	9
α-helix	8	1
β-strand	11-14	4	10
β-strand	24-30	7	9
β-strand	37-43	7	10
β-strand	54-61	8	10
β-strand	66-73	8	10
β-strand	76-77	2	10
β-strand	81-84	4	10
α-helix	87-88	2
β-strand	93-99	7	9
β-strand	103-108	6	9
β-strand	111-117	7	9
α-helix	122-124	3
β-strand	127-132	6	10
β-strand	135-142	8	9
β-strand	146	1	11
β-strand	150-153	4	12
β-strand	159	1	13
β-strand	164-171	8	11
β-strand	177-183	7	12
β-strand	189-196	8	12
β-strand	201-208	8	12
β-strand	211-212	2	12
β-strand	216	1	12
β-strand	229-235	7	11
β-strand	239-244	6	11
β-strand	247-253	7	11
β-strand	261	1	13
β-strand	263-268	6	12
β-strand	270-277	8	11

Chain D: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	8	1
β-strand	11-14	4	10
β-strand	24-31	8	14
β-strand	37-43	7	10
β-strand	54-61	8	10
β-strand	66-73	8	10
β-strand	76-77	2	10
β-strand	81-84	4	10
β-strand	92-99	8	14
β-strand	103-108	6	14
β-strand	111-117	7	14
α-helix	122-124	3
β-strand	127-132	6	10
β-strand	134-142	9	14
β-strand	150-153	4	15
β-strand	164-171	8	16
β-strand	177-183	7	15
β-strand	189-196	8	15
β-strand	201-208	8	15
β-strand	211-212	2	15
β-strand	216	1	15
β-strand	229-235	7	16
β-strand	239-244	6	16
β-strand	247-253	7	16
β-strand	263-268	6	15
β-strand	270-277	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
galectin	A, B, C, D	protein	284	Toxascaris leonina	A0A1L1QJZ7 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5GLZ_1 galectin (chains A, B, C, D)
HHHHHHMATETNYPVPYRSKLTEPFEPGQTLIIKGKTAEDSVRFTINLHNTSADFSGNDV
PLHISVRFDEGKIVFNTFSKGEWGKEERKSNPYKKGDDIDIRIRAHDSKFSISVDQKEVK
EYEHRVPLSSVTHFSVDGDILITYIHWGGKYYPVPYESGLAGDGLAPGKSLLIFATPEKK
GKRFHINLLKKNGDIALHFNPRFDEKAIVRNSLISGEWGNEEREGKNPLEKGIGCDLEFR
NEEYAFQIYVDGERFATYAHRLDPHDINGLQIGGDVEVTGIQMV

Ligands and cofactors

ID	Name	Formula	Copies
BGC	beta-D-glucopyranose	C6 H12 O6	4

Primary citation

Structural Basis for Carbohydrate Recognition and Anti-inflammatory Modulation by Gastrointestinal Nematode Parasite Toxascaris leonina Galectin. Hwang, E.Y., Jeong, M.S., Park, S.K. et al. J Biol Chem (2016) 291:25326-25338. DOI 10.1074/jbc.M116.743773 · PubMed

Other PDB entries of the same protein (UniProt A0A1L1QJZ7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GM0 1.7 Å, Tl-gal with lactose
5GLV 1.8 Å, Tl-gal
5GLT 2.0 Å, Tl-gal with LNT
5GLW 2.0 Å, Tl-gal with LacNAc
5GLU 2.1 Å, Tl-gal with SiaLac
8YZQ 2.15 Å, Toxascaris leonina galectin (Tl-gal) W77F/W212F oligomer
8ZQI 2.98 Å, Glucose bound Toxascaris leonina galectin (Tl-gal) W77F/W212F
8HGJ 4.82 Å, Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3)…

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