9K7I | pdb_00009k7i

Gamma-glutamyl peptidase 1 from Arabidopsis thaliana (Glu complex)

• PDB DOI: https://doi.org/10.2210/pdb9K7I/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• 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: 1.74 Å
• R-Value Free: 
  0.195 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.157 (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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.16 kDa 
• Atom Count: 4,466 
• Modeled Residue Count: 493 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU (Subject of Investigation/LOI)	C [auth A], G [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], E [auth A], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.195 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.289	α = 90
b = 75.816	β = 90
c = 102.772	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