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- PDB-9r3n: The structure of Aspergillus fumigatus phosphoglucose isomerase i... -

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Basic information

Entry
Database: PDB / ID: 9r3n
TitleThe structure of Aspergillus fumigatus phosphoglucose isomerase in complex with fragments
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / PGI / fragment / inhibitor
Function / homology
Function and homology information


glucose-6-phosphate 1-epimerase activity / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / canonical glycolysis / 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
5-PHOSPHOARABINONIC ACID / N-methyl-D-alaninamide / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsYan, K.
Funding support Denmark, United Kingdom, 2items
OrganizationGrant numberCountry
Novo Nordisk Foundation0092593 Denmark
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
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 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,67628
Polymers61,8581
Non-polymers1,81927
Water2,864159
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,35356
Polymers123,7152
Non-polymers3,63754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area20910 Å2
ΔGint-399 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.354, 85.354, 228.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glucose-6-phosphate isomerase


Mass: 61857.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: AFUB_025630 / Production host: Escherichia coli (E. coli) / References: UniProt: B0XS20, glucose-6-phosphate isomerase
#4: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharide / Mass: 246.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H11O9P

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Non-polymers , 5 types, 185 molecules

#2: Chemical
ChemComp-XKD / N-methyl-D-alaninamide


Mass: 102.135 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.4 M citrate, 0.1 M Hepes-NaOH pH 7.5

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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: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.83→60.35 Å / Num. obs: 75344 / % possible obs: 100 % / Redundancy: 25.8 % / CC1/2: 0.999 / Net I/σ(I): 10.3
Reflection shellResolution: 1.83→1.86 Å / Num. unique obs: 3624 / CC1/2: 0.373

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACTdata extraction
xia2data reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→60.35 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.1 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1897 2.7 %RANDOM
Rwork0.18345 ---
obs0.18412 67494 92.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.441 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2--1.76 Å20 Å2
3----3.52 Å2
Refinement stepCycle: 1 / Resolution: 1.83→60.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 100 159 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124464
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163997
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.656049
X-RAY DIFFRACTIONr_angle_other_deg0.5091.5769282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.77513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35610657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
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_it3.2284.4652229
X-RAY DIFFRACTIONr_mcbond_other3.2274.4652229
X-RAY DIFFRACTIONr_mcangle_it4.4076.6992785
X-RAY DIFFRACTIONr_mcangle_other4.4076.6992786
X-RAY DIFFRACTIONr_scbond_it4.1994.7422235
X-RAY DIFFRACTIONr_scbond_other4.2014.7422232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8826.9823264
X-RAY DIFFRACTIONr_long_range_B_refined6.98563.4015065
X-RAY DIFFRACTIONr_long_range_B_other6.89162.7285019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.831→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.759 20 -
Rwork0.745 803 -
obs--15.04 %

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