9S2W | pdb_00009s2w

The structure of phosphoglucose isomerase in complex with deoxynojirimycin-6-phosphate and a fragment

PDB DOI: https://doi.org/10.2210/pdb9S2W/pdb

Classification: ISOMERASE
Organism(s): Candida albicans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-23 Released: 2026-08-12
Deposition Author(s): Yan, K.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Avenues to explore the selectivity of phosphoglucose isomerase inhibitors

Yan, K., Borodkin, V., Ferenbach, A., Fang, W., van Aalten, D.

To be published.

Macromolecule Content

Total Structure Weight: 124.65 kDa
Atom Count: 9,408
Modeled Residue Count: 1,100
Deposited Residue Count: 1,110
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate isomerase	A, B	555	Candida albicans	Mutation(s): 0 Gene Names: PGI1, CAALFM_CR06340CA, CaO19.11369, CaO19.3888 EC: 5.3.1.9 (PDB Primary Data), 5.1.3 (UniProt)
UniProt
Find proteins for P83780 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore P83780 Go to UniProtKB: P83780
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83780
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JCV (Subject of Investigation/LOI) Query on A1JCV Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	[(2~{R},3~{R},4~{R},5~{S})-3,4,5-tris(oxidanyl)piperidin-2-yl]methyl dihydrogen phosphate C₆ H₁₄ N O₇ P GDNPQORLESVKIU-JGWLITMVSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
IRU (Subject of Investigation/LOI) Query on IRU Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth A] H [auth B] C [auth A], D [auth A], E [auth A], G [auth A], H [auth B], I [auth B], J [auth B], L [auth B]	1~{H}-pyrazol-5-ylmethanol C₄ H₆ N₂ O UIEABCXJWANXFS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]