9K7L | pdb_00009k7l

Gamma-glutamyl peptidase 1 from Arabidopsis thaliana (H192N gamma-Glu intermediate)

PDB DOI: https://doi.org/10.2210/pdb9K7L/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.200 (Depositor), 0.208 (DCC)
R-Value Work:
0.166 (Depositor), 0.178 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 60.33 kDa
Atom Count: 4,527
Modeled Residue Count: 499
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-glutamyl peptidase 1	A, B	260	Arabidopsis thaliana	Mutation(s): 1 Gene Names: GGP1, At4g30530 EC: 3.4.19.16
UniProt
Find proteins for Q9M0A7 (Arabidopsis thaliana) Explore Q9M0A7 Go to UniProtKB: Q9M0A7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9M0A7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU (Subject of Investigation/LOI) Query on GLU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	E [auth A], F [auth A], G [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]