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

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Basic information

Entry
Database: PDB / ID: 6xuh
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 / Glycolysis / erythrocyte homeostasis / ciliary membrane ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / humoral immune response / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / cytokine activity / gluconeogenesis / response to progesterone / glycolytic process / TP53 Regulates Metabolic Genes / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / ficolin-1-rich granule lumen / negative regulation of neuron apoptotic process / carbohydrate metabolic process / learning or memory / 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
Chem-O1B / 5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)252,9518
Polymers251,8824
Non-polymers1,0694
Water4,882271
1
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4764
Polymers125,9412
Non-polymers5342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-78 kcal/mol
Surface area37300 Å2
MethodPISA
2
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4764
Polymers125,9412
Non-polymers5342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-83 kcal/mol
Surface area37390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.110, 96.110, 271.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 556 / Label seq-ID: 1 - 556

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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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: saccharide / Mass: 246.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O1B / (2R,3R,4S)-5-((2-aminoethyl)amino)-2,3,4-trihydroxy-5-oxopentyl dihydrogen phosphate


Mass: 288.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
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 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.38→47.32 Å / Num. obs: 97562 / % possible obs: 99.2 % / Redundancy: 3.48 % / CC1/2: 0.995 / Rrim(I) all: 0.119 / Net I/σ(I): 8.12
Reflection shellResolution: 2.38→2.52 Å / Num. unique obs: 15379 / CC1/2: 0.821 / Rrim(I) all: 0.974

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IAT

1iat


Resolution: 2.38→47.32 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 22.48 / SU ML: 0.465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.603 / ESU R Free: 0.339 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3169 4877 5 %RANDOM
Rwork0.2634 ---
obs0.2661 92661 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 223.81 Å2 / Biso mean: 74.73 Å2 / Biso min: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å2-0 Å2-0 Å2
2--3.31 Å2-0 Å2
3----6.62 Å2
Refinement stepCycle: final / Resolution: 2.38→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17748 0 66 271 18085
Biso mean--64.6 42.5 -
Num. residues----2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01918242
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.93924702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.29252220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02324.055868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.763153140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.61415108
X-RAY DIFFRACTIONr_chiral_restr0.0910.22688
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113844
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A370320.04
12B370320.04
21A370440.05
22C370440.05
31A371540.05
32D371540.05
41B369100.05
42C369100.05
51B372440.04
52D372440.04
61C370840.05
62D370840.05
LS refinement shellResolution: 2.38→2.439 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.432 339 -
Rwork0.398 6456 -
obs--93.7 %

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