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- PDB-9rd4: The structure of Candida albicans phosphoglucose isomerase in com... -

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Basic information

Entry
Database: PDB / ID: 9rd4
TitleThe structure of Candida albicans phosphoglucose isomerase in complex with 1-deoxynojirimycin-6-phosphate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Candida / PGI / 1-deoxynojirimycin-6-phosphate
Function / homology
Function and homology information


glucose-6-phosphate 1-epimerase activity / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / fungal biofilm matrix / racemase and epimerase activity, acting on carbohydrates and derivatives / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / canonical glycolysis ...glucose-6-phosphate 1-epimerase activity / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / fungal biofilm matrix / racemase and epimerase activity, acting on carbohydrates and derivatives / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / canonical glycolysis / gluconeogenesis / glycolytic process / mitochondrion / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
: / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsYan, K.
Funding support United Kingdom, Denmark, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
Novo Nordisk Foundation0092593 Denmark
CitationJournal: To Be Published
Title: Avenues to explore the selectivity of phosphoglucose isomerase inhibitors
Authors: Yan, K. / Borodkin, V. / Ferenbach, A. / Fang, W. / van Aalten, D.
History
DepositionJun 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8505
Polymers123,3412
Non-polymers5093
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-85 kcal/mol
Surface area34920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.966, 101.398, 134.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 61670.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: PGI1, CAALFM_CR06340CA, CaO19.11369, CaO19.3888 / Production host: Escherichia coli (E. coli) / References: UniProt: P83780, glucose-6-phosphate isomerase
#2: Chemical ChemComp-A1JCV / [(2~{R},3~{R},4~{R},5~{S})-3,4,5-tris(oxidanyl)piperidin-2-yl]methyl dihydrogen phosphate


Mass: 243.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14NO7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 21 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.71→29.9 Å / Num. obs: 124894 / % possible obs: 96.7 % / Redundancy: 11.9 % / CC1/2: 0.999 / Net I/σ(I): 17.7
Reflection shellResolution: 1.71→1.74 Å / Num. unique obs: 4627 / CC1/2: 0.779

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→29.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.95 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 6343 5.1 %RANDOM
Rwork0.18325 ---
obs0.18469 118171 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.332 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0 Å2
2---0.86 Å20 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.71→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8607 0 31 636 9274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128877
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167986
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.64512051
X-RAY DIFFRACTIONr_angle_other_deg0.8581.5718597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64351112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.162526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.761101430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.21345
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021811
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4371.644412
X-RAY DIFFRACTIONr_mcbond_other1.4351.644412
X-RAY DIFFRACTIONr_mcangle_it1.9272.4555515
X-RAY DIFFRACTIONr_mcangle_other1.9282.4565516
X-RAY DIFFRACTIONr_scbond_it2.2741.8424465
X-RAY DIFFRACTIONr_scbond_other2.2731.8424465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3342.6716530
X-RAY DIFFRACTIONr_long_range_B_refined4.12321.61110466
X-RAY DIFFRACTIONr_long_range_B_other4.02621.24310331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.75 Å
RfactorNum. reflection% reflection
Rfree0.276 349 -
Rwork0.232 6799 -
obs--75.75 %

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