3D32: PDB entry 3D32

Complex of GABA(A) receptor-associated protein (GABARAP) with a synthetic peptide. Determined by X-ray diffraction at 1.3 Å resolution. Released 5 Aug 2008.

Method: X-ray diffraction
Resolution: 1.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 2,599
Mol. weight: 31.46 kDa
Released: 5 Aug 2008

Explore 3D32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D32 contains 13 α-helices and 16 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	13-26	14
β-strand	30-37	8	1
α-helix	44-46	3
β-strand	50-54	5	1
β-strand	58	1	2
α-helix	59-70	12
β-strand	79-81	3	1
β-strand	82	1	3
β-strand	85	1	3
β-strand	92	1	2
α-helix	93-100	8
β-strand	107-112	6	1

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	13-26	14
β-strand	30-37	8	4
α-helix	44-46	3
β-strand	50-54	5	4
β-strand	58	1	5
α-helix	59-69	11
α-helix	72-73	2
β-strand	79-81	3	4
β-strand	82	1	6
β-strand	85	1	6
β-strand	92	1	5
α-helix	93-100	8
β-strand	107-112	6	4

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor-associated protein	A, B	protein	119	Homo sapiens	O95166 (AlphaFold model)
K1 peptide	C, D	protein	13	synthetic construct

Sequence of entity 1 (A, B), FASTA

>3D32_1 Gamma-aminobutyric acid receptor-associated protein (chains A, B)
GSMKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVG
QFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL

Sequence of entity 2 (C, D), FASTA

>3D32_2 K1 peptide (chains C, D)
DATYTWEHLAWPX

Primary citation

Ligand Binding Mode of GABA(A) Receptor-Associated Protein. Weiergraber, O.H., Stangler, T., Thielmann, Y. et al. J Mol Biol (2008) 381:1320-1331. DOI 10.1016/j.jmb.2008.06.086 · 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
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
6HOJ 1.51 Å, Structure of Beclin1 LIR motif bound to GABARAP

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