9HGD: Human GABARAP

Crystal structure of human GABARAP in complex with cyclic peptide GAB_D23. Determined by X-ray diffraction at 1.5 Å resolution. Released 9 Jul 2025.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 2,714
Mol. weight: 31.89 kDa
Released: 9 Jul 2025

Explore 9HGD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HGD contains 15 α-helices and 18 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	11-24	14
β-strand	28-35	8	1
α-helix	36	1
β-strand	48-52	5	1
β-strand	56	1	2
α-helix	57-68	12
β-strand	77-79	3	1
β-strand	80	1	3
β-strand	83	1	3
α-helix	84-86	3
β-strand	90	1	2
α-helix	91-98	8
β-strand	105-110	6	1

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6-7	2	1

Chain C: 8 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
α-helix	42-44	3
β-strand	48-52	5	4
β-strand	56	1	5
α-helix	57-67	11
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
α-helix	104	1
β-strand	105-110	6	4

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	5-7	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor-associated protein	A, C	protein	119	Homo sapiens	O95166 (AlphaFold model)
GAB_D23	B, D	protein	13	synthetic construct

Sequence of entity 1 (A, C), FASTA

>9HGD_1 Gamma-aminobutyric acid receptor-associated protein (chains A, C)
GSMKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVG
QFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL

Sequence of entity 2 (B, D), FASTA

>9HGD_2 GAB_D23 (chains B, D)
LEDGWVDIETGKE

Primary citation

Accurate de novo design of high-affinity protein-binding macrocycles using deep learning. Rettie, S.A., Juergens, D., Adebomi, V. et al. Nat Chem Biol (2025) 21:1948-1956. DOI 10.1038/s41589-025-01929-w · 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
6HOJ 1.51 Å, Structure of Beclin1 LIR motif bound to GABARAP

Browse structure collections

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