4HAN: Galectin 8 with NDP52 peptide

Crystal structure of Galectin 8 with NDP52 peptide. Determined by X-ray diffraction at 2.55 Å resolution. Released 20 Mar 2013.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,257
Mol. weight: 71.02 kDa
Ligands: NAD
Released: 20 Mar 2013

Explore 4HAN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HAN contains 10 α-helices and 55 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: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	1-13	13	1
β-strand	19-22	4	2
β-strand	32-38	7	1
β-strand	45-51	7	2
β-strand	56	1	3
β-strand	59	1	3
α-helix	60-61	2
β-strand	62-69	8	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	145-155	11	1
α-helix	156-184	3
β-strand	187-190	4	4
β-strand	200-207	8	1
β-strand	213-220	8	4
β-strand	225-233	9	4
β-strand	238-245	8	4
β-strand	248-249	2	4
β-strand	253	1	4
β-strand	266-273	8	1
β-strand	277-282	6	1
β-strand	285-291	7	1
α-helix	297-299	3
β-strand	302-307	6	4
β-strand	309-316	8	1

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	1-13	13	1
β-strand	19-22	4	5
β-strand	31-38	8	1
β-strand	45-51	7	5
β-strand	56	1	6
β-strand	59	1	6
α-helix	60	1
β-strand	62-69	8	5
β-strand	75-82	8	5
β-strand	85-86	2	5
β-strand	90-92	3	5
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	5
β-strand	145-155	11	1
α-helix	156	1
β-strand	157	1	1
α-helix	184	1
β-strand	187-190	4	7
β-strand	200-207	8	1
β-strand	213-220	8	7
β-strand	225-233	9	7
α-helix	234-236	3
β-strand	238-245	8	7
β-strand	248-249	2	7
β-strand	253	1	7
β-strand	266-273	8	1
β-strand	277-282	6	1
β-strand	285-291	7	1
α-helix	297-299	3
β-strand	302-307	6	7
β-strand	309-316	8	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Galectin-8	A, B	protein	293	Homo sapiens	O00214 (AlphaFold model)
Calcium-binding and coiled-coil domain-containing protein 2	C, D	protein	14	Homo sapiens	Q13137 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4HAN_1 Galectin-8 (chains A, B)
GSMMLSLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSVKP
RADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAV
NGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSSHMRLPFAARLNTPMGPGRTVVVK
GEVNANAKSFNVDLLAGKSKDIALHLNPRLNIKAFVRNSFLQESWGEEERNITSFPFSPG
MYFEMIIYCDVREFKVAVNGVHSLEYKHRFKELSSIDTLEINGDIHLLEVRSW

Sequence of entity 2 (C, D), FASTA

>4HAN_2 Calcium-binding and coiled-coil domain-containing protein 2 (chains C, D)
PGLAYGNPYSGIQE

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	2

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

Primary citation

Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8. Kim, B.W., Hong, S.B., Kim, J.H. et al. Nat Commun (2013) 4:1613-1613. DOI 10.1038/ncomms2606 · 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…
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…

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