5DPT: PLEKHM1 LIR-fused human GABARAPL1_2-117

Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117. Determined by X-ray diffraction at 2.9 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,949
Mol. weight: 31.65 kDa
Released: 28 Sept 2016

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

Secondary structure: helices and β-sheets

5DPT contains 14 α-helices and 18 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: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4-5	2	1
α-helix	12-15	4
α-helix	18-31	14
β-strand	35-42	8	2
α-helix	49-51	3
β-strand	55-59	5	2
β-strand	63	1	3
α-helix	64-75	12
β-strand	84-86	3	2
β-strand	87	1	4
β-strand	90	1	4
α-helix	91-93	3
β-strand	97	1	3
α-helix	98-105	8
β-strand	106	1	2
β-strand	112-117	6	2

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	12-15	4
α-helix	18-31	14
β-strand	35-42	8	1
α-helix	43	1
β-strand	55-59	5	1
β-strand	63	1	5
α-helix	64-75	12
β-strand	84-86	3	1
β-strand	87	1	6
β-strand	90	1	6
α-helix	91-93	3
β-strand	97	1	5
α-helix	98-105	8
β-strand	112-117	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid…	A, B	protein	132	Homo sapiens	Q9H0R8 (AlphaFold model), Q9Y4G2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DPT_1 Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1 (chains A, B)
GSVRPQQEDEWVNVGSKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLD
KRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFL
YVAYSDESVYGK

Primary citation

Structural and functional analysis of the GABARAP interaction motif (GIM). Rogov, V.V., Stolz, A., Ravichandran, A.C. et al. EMBO Rep (2017) 18:1382-1396. DOI 10.15252/embr.201643587 · PubMed

Other PDB entries of the same protein (UniProt Q9H0R8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YOO 1.06 Å, Structure of SAMM50 LIR bound to GABARAPL1
6HOI 1.14 Å, Structure of Beclin1 LIR motif bound to GABARAPL1
6HOL 1.4 Å, Structure of ATG14 LIR motif bound to GABARAPL1
5LXI 1.44 Å, GABARAP-L1 ATG4B LIR Complex
7AA7 1.45 Å, Structure of SCOC pS12/pS18 LIR motif bound to GABARAPL1
8X8A 1.53 Å, Crystal structure of STBD1 LIR motif in complex with GABARAPL1
5LXH 1.58 Å, GABARAP-L1 ATG4B LIR Complex
2R2Q 1.65 Å, Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1…
7AA9 1.72 Å, Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1
9JF2 1.76 Å, Crystal structure of GABARAPL1 in complex with ATG16L1
7JHX 1.91 Å, Crystal structure of hEPG5 LIR/GABARAPL1 complex
9HGC 2.52 Å, Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8

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