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- PDB-9r5u: The structure of CaPGI in complex with fragments -

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Basic information

Entry
Database: PDB / ID: 9r5u
TitleThe structure of CaPGI in complex with fragments
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / Candida / fragment / PGI
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 / glycolytic process / gluconeogenesis / 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
: / N-propan-2-ylurea / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYan, K.
Funding support United Kingdom, Denmark, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
Wellcome Trust200208/Z/15/Z United Kingdom
Novo Nordisk Foundation0092593 Denmark
CitationJournal: To Be Published
Title: 1-Deoxynojirimycin-6-phosphate is a tool to explore selectivity of inhibitors against phosphoglucose isomerase in Aspergillus fumigatus
Authors: Yan, K. / Borodkin, V. / Fang, W. / van Aalten, D.
History
DepositionMay 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)124,92616
Polymers123,3412
Non-polymers1,58514
Water13,277737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-85 kcal/mol
Surface area34020 Å2
Unit cell
Length a, b, c (Å)87.310, 101.440, 139.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 751 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical
ChemComp-XH1 / N-propan-2-ylurea


Mass: 102.135 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.75 %
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: 1.7→59.76 Å / Num. obs: 135074 / % possible obs: 99.3 % / Redundancy: 11.4 % / CC1/2: 0.998 / Net I/σ(I): 8.7
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 6135 / CC1/2: 0.344

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Processing

Software
NameVersionClassification
REFMAC8.0.004refinement
xia2data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→59.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.958 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22063 6685 5 %RANDOM
Rwork0.18422 ---
obs0.186 128132 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.809 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0 Å2
2---0.67 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.7→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8604 0 102 737 9443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0128922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168038
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.64712098
X-RAY DIFFRACTIONr_angle_other_deg0.6151.58118698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63251106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.94526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.172101434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021823
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_it1.4741.9984406
X-RAY DIFFRACTIONr_mcbond_other1.4741.9984406
X-RAY DIFFRACTIONr_mcangle_it1.9952.995506
X-RAY DIFFRACTIONr_mcangle_other1.9952.995507
X-RAY DIFFRACTIONr_scbond_it2.6262.2494516
X-RAY DIFFRACTIONr_scbond_other2.6252.2494517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9143.2546589
X-RAY DIFFRACTIONr_long_range_B_refined4.74525.76310383
X-RAY DIFFRACTIONr_long_range_B_other4.61824.97110211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 449 -
Rwork0.411 8670 -
obs--91.04 %

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