9FOS | pdb_00009fos

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

PDB DOI: https://doi.org/10.2210/pdb9FOS/pdb

Classification: LYASE
Organism(s): Leishmania infantum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-06-12 Released: 2025-06-25
Deposition Author(s): Fiorillo, A., Ilari, A., Bibi, A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.240 (Depositor), 0.245 (DCC)
R-Value Work:
0.193 (Depositor), 0.199 (DCC)

Starting Model: integrative
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Fiorillo, A., Ilari, A., Bibi, A.

To be published.

Macromolecule Content

Total Structure Weight: 80 kDa
Atom Count: 3,476
Modeled Residue Count: 440
Deposited Residue Count: 727
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ornithine decarboxylase	A	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

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMO (Subject of Investigation/LOI) Query on DMO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ALPHA-DIFLUOROMETHYLORNITHINE C₆ H₁₂ F₂ N₂ O₂ VLCYCQAOQCDTCN-ZCFIWIBFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.240 (Depositor), 0.245 (DCC)
R-Value Work: 0.193 (Depositor), 0.199 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.87	α = 90
b = 117.87	β = 90
c = 82.175	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Italy	--

Revision History (Full details and data files)

Version 1.0: 2025-06-25
Type: Initial release
Version 1.1: 2025-07-02
Changes: Database references, Structure summary

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.