9I9X | pdb_00009i9x

Human GABARAP in complex with artificial peptide IM-2

• PDB DOI: https://doi.org/10.2210/pdb9I9X/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-07 Released: 2026-02-18 
• Deposition Author(s): Wilms, J.A., McDonald, I., Willbold, D., Kritzer, J.A., Weiergraeber, O.H.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.197 (Depositor) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Human GABARAP in complex with artificial peptide IM-2

McDonald, I., Wilms, J.A., Weiergraeber, O.H., Kritzer, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.76 kDa 
• Atom Count: 1,538 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor-associated protein	A	119	Homo sapiens	Mutation(s): 0  Gene Names: GABARAP, FLC3B, HT004
UniProt & NIH Common Fund Data Resources
Find proteins for O95166 (Homo sapiens) Explore O95166  Go to UniProtKB:  O95166
PHAROS:  O95166 GTEx:  ENSG00000170296

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
artificial peptide IM-2	B	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.197 (Depositor) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.15151/ESRF-DC-2039871972

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.34	α = 90
b = 101.34	β = 90
c = 101.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Wilms, J.A., McDonald, I., Willbold, D., Kritzer, J.A., Weiergraeber, O.H.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	267205415-SFB 1208

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release