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- PDB-6xui: Crystal structure of human phosphoglucose isomerase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6xui
TitleCrystal structure of human phosphoglucose isomerase in complex with inhibitor
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / enzyme inhibitor / phosphate / monosaccharide / phosphoglucose isomerase / autocrine motility factor
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / erythrocyte homeostasis / Glycolysis / ciliary membrane ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / erythrocyte homeostasis / Glycolysis / ciliary membrane / response to testosterone / humoral immune response / positive regulation of immunoglobulin production / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / gluconeogenesis / TP53 Regulates Metabolic Genes / glycolytic process / growth factor activity / glucose homeostasis / response to estradiol / secretory granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / ficolin-1-rich granule lumen / learning or memory / carbohydrate metabolic process / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / 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 / Chem-PG6 / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi de la Sierra-Gallay, I. / Ahmad, L. / Plancqueel, S. / van Tilbeurgh, H. / Salmon, L.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-33 France
French Infrastructure for Integrated Structural Biology (FRISBI)FRISBI ANR-10-INSB-0501 France
CitationJournal: Bioorg.Chem. / Year: 2020
Title: Novel N-substituted 5-phosphate-d-arabinonamide derivatives as strong inhibitors of phosphoglucose isomerases: Synthesis, structure-activity relationship and crystallographic studies.
Authors: Ahmad, L. / Plancqueel, S. / Lazar, N. / Korri-Youssoufi, H. / Li de la Sierra-Gallay, I. / van Tilbeurgh, H. / Salmon, L.
History
DepositionJan 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,11614
Polymers251,8824
Non-polymers2,23410
Water25,2571402
1
A: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9666
Polymers125,9412
Non-polymers1,0254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1508
Polymers125,9412
Non-polymers1,2096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.551, 106.947, 270.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glucose-6-phosphate isomerase / / GPI / Autocrine motility factor / AMF / Neuroleukin / NLK / Phosphoglucose isomerase / PGI / ...GPI / Autocrine motility factor / AMF / Neuroleukin / NLK / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI / Sperm antigen 36 / SA-36


Mass: 62970.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPI / Production host: Escherichia coli (E. coli) / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Sugar
ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharideCarbohydrate / Mass: 246.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, magnesium chloride, TRIS-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.95→48.26 Å / Num. obs: 170097 / % possible obs: 99.3 % / Redundancy: 3.69 % / CC1/2: 0.998 / Rrim(I) all: 0.109 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→2.07 Å / Num. unique obs: 26904 / CC1/2: 0.981 / Rrim(I) all: 111.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IAT

1iat


Resolution: 1.95→48.26 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.781 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 8505 5 %RANDOM
Rwork0.1707 ---
obs0.1728 161583 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.42 Å2 / Biso mean: 29.936 Å2 / Biso min: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--2.95 Å20 Å2
3----2.01 Å2
Refinement stepCycle: final / Resolution: 1.95→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17748 0 144 1402 19294
Biso mean--43.92 37.27 -
Num. residues----2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01318314
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716848
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.64424770
X-RAY DIFFRACTIONr_angle_other_deg1.4111.57639112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61552220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77122.5976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.891153140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.24115108
X-RAY DIFFRACTIONr_chiral_restr0.0730.22348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023912
LS refinement shellResolution: 1.95→1.998 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.398 601 -
Rwork0.386 11415 -
obs--96.01 %

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