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

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
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Ligand Structure Quality Assessment

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Literature

Sucrose-phosphate synthase from Leishmania major

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QES5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth B] mmCIF format, chain F [auth C]	D [auth B], F [auth C]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain D [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth B] Focus chain F [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain E [auth C] MOL2 format, chain C [auth B] MOL2 format, chain E [auth C] mmCIF format, chain C [auth B] mmCIF format, chain E [auth C]	C [auth B], E [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain E [auth C] Interactions & Density Focus chain C [auth B] Focus chain E [auth C]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

McConville, M.J.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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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.