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- PDB-2wbd: FRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE-1- PHOSPH... -

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Basic information

Entry
Database: PDB / ID: 2wbd
TitleFRUCTOSE-1,6-BISPHOSPHATASE(D-FRUCTOSE-1,6-BISPHOSPHATE-1- PHOSPHOHYDROLASE) (E.C.3.1.3.11) COMPLEXED WITH AN AMP SITE INHIBITOR
ComponentsFRUCTOSE-1,6-BISPHOSPHATASE 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE / PHOSPHORIC MONOESTER / ALLOSTERIC ENZYME / CARBOHYDRATE METABOLISM / GLUCONEOGENESIS
Function / homology
Function and homology information


cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-RO5 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRuf, A. / Joseph, C. / Benz, J. / Fol, B. / Tetaz, T. / Kitas, E. / Mohr, P. / Kuhn, B. / Wessel, H.P. / Hebeisen, P. ...Ruf, A. / Joseph, C. / Benz, J. / Fol, B. / Tetaz, T. / Kitas, E. / Mohr, P. / Kuhn, B. / Wessel, H.P. / Hebeisen, P. / Haap, W. / Huber, W. / Alvarez Sanchez, R. / Paehler, A. / Bernadeau, A. / Gubler, M. / Schott, B. / Tozzo, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Sulfonylureido Thiazoles as Fructose-1,6-Bisphosphatase Inhibitors for the Treatment of Type-2 Diabetes.
Authors: Kitas, E. / Mohr, P. / Kuhn, B. / Wessel, H.P. / Hebeisen, P. / Haap, W. / Ruf, A. / Benz, J. / Joseph, C. / Huber, W. / Alvarez Sanchez, R. / Paehler, A. / Bernadeau, A. / Gubler, M. / Schott, B. / Tozzo, E.
History
DepositionFeb 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-1,6-BISPHOSPHATASE 1
B: FRUCTOSE-1,6-BISPHOSPHATASE 1
C: FRUCTOSE-1,6-BISPHOSPHATASE 1
D: FRUCTOSE-1,6-BISPHOSPHATASE 1
E: FRUCTOSE-1,6-BISPHOSPHATASE 1
F: FRUCTOSE-1,6-BISPHOSPHATASE 1
G: FRUCTOSE-1,6-BISPHOSPHATASE 1
H: FRUCTOSE-1,6-BISPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,99816
Polymers294,8758
Non-polymers3,1228
Water9,620534
1
A: FRUCTOSE-1,6-BISPHOSPHATASE 1
B: FRUCTOSE-1,6-BISPHOSPHATASE 1
C: FRUCTOSE-1,6-BISPHOSPHATASE 1
D: FRUCTOSE-1,6-BISPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9998
Polymers147,4384
Non-polymers1,5614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19180 Å2
ΔGint-133.6 kcal/mol
Surface area54870 Å2
MethodPQS
2
E: FRUCTOSE-1,6-BISPHOSPHATASE 1
F: FRUCTOSE-1,6-BISPHOSPHATASE 1
G: FRUCTOSE-1,6-BISPHOSPHATASE 1
H: FRUCTOSE-1,6-BISPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,9998
Polymers147,4384
Non-polymers1,5614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18780 Å2
ΔGint-93.3 kcal/mol
Surface area54460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.842, 285.402, 83.552
Angle α, β, γ (deg.)90.00, 97.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 500
2115B1 - 500
3115C1 - 500
4115D1 - 500
5115E1 - 500
6115F1 - 500
7115G1 - 500
8115H1 - 500

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Components

#1: Protein
FRUCTOSE-1,6-BISPHOSPHATASE 1 / Fructose 1,6-bisphosphatase / D-FRUCTOSE-1\ / 6-BISPHOSPHATE 1-PHOSPHOHYDROLASE 1 / FBPASE 1


Mass: 36859.418 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical
ChemComp-RO5 / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-3-ethylbenzenesulfonamide


Mass: 390.276 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H12BrN3O3S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 55.68 % / Description: NONE
Crystal growDetails: 0.1M AMMONIUM ACETATE, 0.1M HEPES PH 7.0, 15% PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 237087 / % possible obs: 99.1 % / Redundancy: 1.95 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.28
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WBB

2wbb


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.88 / SU B: 10.911 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27684 6014 5 %RANDOM
Rwork0.21987 ---
obs0.22276 114172 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.684 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å20 Å2-0.07 Å2
2---0.88 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19440 0 168 534 20142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02219993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.99927009
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99852524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97324.264774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.046153561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.44215102
X-RAY DIFFRACTIONr_chiral_restr0.0890.23062
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114774
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6021.512604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.145220293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.59337389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6214.56716
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1268medium positional0.280.5
2B1268medium positional0.280.5
3C1268medium positional0.40.5
4D1268medium positional0.270.5
5E1268medium positional0.240.5
6F1268medium positional0.270.5
7G1268medium positional0.390.5
8H1268medium positional0.280.5
1A1173loose positional0.625
2B1173loose positional0.725
3C1173loose positional0.755
4D1173loose positional0.655
5E1173loose positional0.65
6F1173loose positional0.675
7G1173loose positional0.755
8H1173loose positional0.695
1A1268medium thermal2.022
2B1268medium thermal3.082
3C1268medium thermal4.212
4D1268medium thermal5.992
5E1268medium thermal5.412
6F1268medium thermal5.572
7G1268medium thermal2.92
8H1268medium thermal2.712
1A1173loose thermal2.5610
2B1173loose thermal3.3610
3C1173loose thermal4.3610
4D1173loose thermal6.0310
5E1173loose thermal5.4910
6F1173loose thermal5.5710
7G1173loose thermal3.1910
8H1173loose thermal3.2610
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 436 -
Rwork0.303 8339 -
obs--99.99 %

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