9K7K | pdb_00009k7k

Gamma-glutamyl peptidase 1 from Arabidopsis thaliana (inactive form)

• PDB DOI: https://doi.org/10.2210/pdb9K7K/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-23 Released: 2025-10-29 
• Deposition Author(s): Sone, K., Kashima, T., Miyanaga, A., Fushinobu, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.233 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

Crystal structures of Gamma-glutamyl peptidase 1 from Arabidopsis thaliana

Sone, K., Ito, T., Yamada, C., Kashima, T., Miyanaga, A., Ohkama-Ohtsu, N., Fushinobu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 59.87 kDa 
• Atom Count: 4,163 
• Modeled Residue Count: 491 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-glutamyl peptidase 1	A, B	260	Arabidopsis thaliana	Mutation(s): 0  Gene Names: GGP1, At4g30530 EC: 3.4.19.16
UniProt
Find proteins for Q9M0A7 (Arabidopsis thaliana) Explore Q9M0A7  Go to UniProtKB:  Q9M0A7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.233 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.354	α = 90
b = 75.329	β = 90
c = 102.583	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Sone, K., Kashima, T., Miyanaga, A., Fushinobu, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release