9GYG | pdb_00009gyg

The structure of ornithine decarboxylase from Leishmania infantum in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb9GYG/pdb
EM Map EMD-51698: EMDB EMDataResource

Classification: LYASE
Organism(s): Leishmania infantum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-02 Released: 2025-10-15
Deposition Author(s): Fiorillo, A., Antonelli, A., Ilari, A., Tria, G.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The structure of ornithine decarboxylase from Leishmania infantum in complex with PLP

Fiorillo, A., Antonelli, A., Ilari, A., Tria, G.

To be published.

Macromolecule Content

Total Structure Weight: 159.6 kDa
Atom Count: 7,214
Modeled Residue Count: 908
Deposited Residue Count: 1,454
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ornithine decarboxylase	A, B	727	Leishmania infantum	Mutation(s): 0 Gene Names: LINJ.12.0100 EC: 4.1.1.17
UniProt
Find proteins for E9AGB5 (Leishmania infantum) Explore E9AGB5 Go to UniProtKB: E9AGB5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E9AGB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Italy	RM123188F763A9D5

Revision History (Full details and data files)

Version 1.0: 2025-10-15
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.