7ZKR: Human GABARAP

Human GABARAP in complex with stapled peptide Pen3-ortho. Determined by X-ray diffraction at 1.1 Å resolution. Released 31 Aug 2022.

Method: X-ray diffraction
Resolution: 1.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,551
Mol. weight: 16.02 kDa
Ligands: OXE, PO4
Released: 31 Aug 2022

Explore 7ZKR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZKR contains 7 α-helices and 9 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: 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	42-44	3
β-strand	48-52	5	1
β-strand	56	1	2
α-helix	57-67	11
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	7-9	3
β-strand	10	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor-associated protein	A	protein	119	Homo sapiens	O95166 (AlphaFold model)
Pen3-ortho	B	protein	14	synthetic construct

Sequence of entity 1 (A), FASTA

>7ZKR_1 Gamma-aminobutyric acid receptor-associated protein (chains A)
GSMKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVG
QFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL

Sequence of entity 2 (B), FASTA

>7ZKR_2 Pen3-ortho (chains B)
XDAXYTWECLAWPX

Ligands and cofactors

ID	Name	Formula	Copies
OXE	Ortho-xylene	C8 H10	1
PO4	Phosphate ion	O4 P	3

Water and common crystallization additives (CL) are not listed.

Primary citation

Structure-Based Design of Stapled Peptides That Bind GABARAP and Inhibit Autophagy. Brown, H., Chung, M., Uffing, A. et al. J Am Chem Soc (2022) 144:14687-14697. DOI 10.1021/jacs.2c04699 · 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
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
6HOJ 1.51 Å, Structure of Beclin1 LIR motif bound to GABARAP

Browse structure collections

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