5DPS: PLEKHM1 LIR-fused human GABARAP_2-117

Crystal structure of PLEKHM1 LIR-fused human GABARAP_2-117. Determined by X-ray diffraction at 2.0 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,167
Mol. weight: 46.74 kDa
Released: 28 Sept 2016

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

Secondary structure: helices and β-sheets

5DPS contains 19 α-helices and 28 β-strands across 3 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	11-15	5
α-helix	18-31	14
β-strand	35-42	8	1
α-helix	49-51	3
β-strand	55-59	5	1
β-strand	63	1	2
α-helix	64-75	12
β-strand	84-86	3	1
β-strand	87	1	3
β-strand	90	1	3
β-strand	97	1	2
α-helix	98-105	8
β-strand	112-117	6	1

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5	1	4
α-helix	11-15	5
α-helix	18-31	14
β-strand	35-42	8	5
α-helix	49-51	3
β-strand	55-59	5	5
β-strand	63	1	6
α-helix	64-74	11
β-strand	84-86	3	5
β-strand	87	1	7
β-strand	90	1	7
α-helix	91-93	3
β-strand	97	1	6
α-helix	98-105	8
β-strand	107	1	4
β-strand	112-117	6	5

Chain C: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4	1	8
α-helix	10-13	4
α-helix	17-30	14
β-strand	34-41	8	9
α-helix	48-50	3
β-strand	54-58	5	9
β-strand	62	1	10
α-helix	63-73	11
β-strand	83-85	3	9
β-strand	86	1	11
β-strand	89	1	11
β-strand	96	1	10
α-helix	97-104	8
β-strand	106	1	8
β-strand	111-116	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pleckstrin homology domain-containing family M member 1,Gamma-aminobutyric acid…	A, B, C	protein	132	Homo sapiens	O95166 (AlphaFold model), Q9Y4G2 (AlphaFold model)

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

>5DPS_1 Pleckstrin homology domain-containing family M member 1,Gamma-aminobutyric acid receptor-associated protein (chains A, B, C)
GSVRPQQEDEWVNVGSKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLD
KKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFL
YIAYSDESVYGL

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 O95166 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HYO 1.07 Å, Structure of ULK1 LIR motif bound to GABARAP
6YOP 1.1 Å, Structure of SAMM50 LIR bound to GABARAP
7ZKR 1.1 Å, Human GABARAP in complex with stapled peptide Pen3-ortho
6HYN 1.14 Å, Structure of ATG13 LIR motif bound to GABARAP
7AA8 1.25 Å, Structure of SCOC LIR bound to GABARAP
6HOG 1.26 Å, Structure of VPS34 LIR motif bound to GABARAP
8T2M 1.27 Å, Crystal structure of GABARAP in complex with the LIR of NSs4
3D32 1.3 Å, Complex of GABA(A) receptor-associated protein (GABARAP) with a synthetic peptide
6HB9 1.3 Å, Crystal structure of the GABARAP in complex with the UBA5 LIR motif
7BRQ 1.4 Å, Crystal structure of human FAM134B LIR fused to human GABARAP
9I9X 1.42 Å, Human GABARAP in complex with artificial peptide IM-2
9HGD 1.5 Å, Crystal structure of human GABARAP in complex with cyclic peptide GAB_D23

Browse structure collections

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