5YIR: AnkB LIR/GABARAP complex

Crystal Structure of AnkB LIR/GABARAP complex. Determined by X-ray diffraction at 2.75 Å resolution. Released 23 May 2018.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 3,344
Mol. weight: 52.12 kDa
Ligands: NI
Released: 23 May 2018

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

Secondary structure: helices and β-sheets

5YIR contains 21 α-helices and 27 β-strands across 6 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.

Chains A, B and D: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	11-24	14
β-strand	28-35	8	4
α-helix	36	1
β-strand	48-52	5	4
β-strand	56	1	5
α-helix	57-68	12
β-strand	77-79	3	4
β-strand	80	1	6
β-strand	83	1	6
α-helix	84-86	3
β-strand	90	1	5
α-helix	91-98	8
β-strand	105-110	6	4

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1990-1991	2	1
α-helix	1994-2002	9

Chains G and H: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1990-1991	2	4
α-helix	1994-2003	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor-associated protein	A, B, D	protein	117	Mus musculus	Q9DCD6 (AlphaFold model)
Ankyrin-2	C, G, H	protein	27	Homo sapiens	Q01484 (AlphaFold model)

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

>5YIR_1 Gamma-aminobutyric acid receptor-associated protein (chains A, B, D)
MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQF
YFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL

Sequence of entity 2 (C, G, H), FASTA

>5YIR_2 Ankyrin-2 (chains C, G, H)
VEEEWVIVSDEEIEEARQKAPLEITEY

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	10

Primary citation

Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins. Li, J., Zhu, R., Chen, K. et al. Nat Chem Biol (2018) 14:778-787. DOI 10.1038/s41589-018-0082-8 · PubMed

Other PDB entries of the same protein (UniProt Q9DCD6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6A9X 2.2 Å, Crystal Structure of AnkG/GABARAP Complex
7FB5 2.84 Å, Crystal structure of FAM134B/GABARAP complex

Browse structure collections

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