8VRF | pdb_00008vrf

Sucrose-phosphate synthase-like protein from Leishmania major

PDB DOI: https://doi.org/10.2210/pdb8VRF/pdb

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

Deposited: 2024-01-21 Released: 2025-08-13
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: 1.74 Å
R-Value Free:
0.211 (Depositor), 0.214 (DCC)
R-Value Work:
0.179 (Depositor), 0.188 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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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

Sucrose-phosphate synthase-like protein from Leishmania major

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

To be published.

Macromolecule Content

Total Structure Weight: 106.93 kDa
Atom Count: 8,122
Modeled Residue Count: 911
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose-phosphate synthase-like protein	A [auth B], B [auth A]	464	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4QES5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG (Subject of Investigation/LOI) Query on UPG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain H [auth B] MOL2 format, chain N [auth A] MOL2 format, chain H [auth B] mmCIF format, chain N [auth A] mmCIF format, chain H [auth B]	H [auth B], N [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain H [auth B] Focus chain N [auth A] Interactions & Density Focus chain H [auth B] Focus chain N [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	E [auth B] F [auth B] G [auth B] J [auth A] K [auth A] E [auth B], F [auth B], G [auth B], J [auth A], K [auth A], L [auth A], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain I [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain I [auth A]	C [auth B], D [auth B], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain I [auth A]