9DCM | pdb_00009dcm

Sucrose-phosphate synthase from Leishmania major

• PDB DOI: https://doi.org/10.2210/pdb9DCM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-27 Released: 2025-10-29 
• Deposition Author(s): Gorman, M.A., Parker, M.W., McConville, M.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 
  0.228 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Sucrose-phosphate synthase from Leishmania major

Gorman, M.A., Parker, M.W., McConville, M.J.

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 Evidence: gel filtration

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: 105.52 kDa 
• Atom Count: 7,373 
• Modeled Residue Count: 918 
• Deposited Residue Count: 924 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose-phosphate synthase-like protein	A [auth B], B [auth C]	462	Leishmania major	Mutation(s): 0  Gene Names: LMJF_16_0950 EC: 2.4.1.14
UniProt
Find proteins for Q4QES5 (Leishmania major) Explore Q4QES5  Go to UniProtKB:  Q4QES5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	D [auth B], F [auth C]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
CA	C [auth B], E [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free:  0.228 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.895	α = 90
b = 216.895	β = 90
c = 216.895	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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): Gorman, M.A., Parker, M.W., McConville, M.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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