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- PDB-2fix: Structure of human liver FBPase complexed with potent benzoxazole... -

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Basic information

Entry
Database: PDB / ID: 2fix
TitleStructure of human liver FBPase complexed with potent benzoxazole allosteric inhibitiors
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / allosteric inhibitors human liver FBPase / benzoxazole / intersubunit allosteric inhibitors of human liver FBPase
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 / monosaccharide binding / negative regulation of glycolytic process / fructose 1,6-bisphosphate metabolic 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 / nucleus / metal ion binding / cytoplasm / cytosol
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-870 / : / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsAbad-Zapatero, C.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Benzoxazole benzenesulfonamides as allosteric inhibitors of fructose-1,6-bisphosphatase.
Authors: Lai, C. / Gum, R.J. / Daly, M. / Fry, E.H. / Hutchins, C. / Abad-Zapatero, C. / von Geldern, T.W.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Benzoxazole benzenesulfonamides are novel allosteric inhibitors of fructose-1,6-bisphosphatase with a distinct binding mode.
Authors: von Geldern, T.W. / Lai, C. / Gum, R.J. / Daly, M. / Sun, C. / Fry, E.H. / Abad-Zapatero, C.
History
DepositionDec 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN REGARDING THE LIGAND 870, THE USER SHOULD REFER TO COMPOUND NO. 53 IN THE MAIN REFERENCE ...HETEROGEN REGARDING THE LIGAND 870, THE USER SHOULD REFER TO COMPOUND NO. 53 IN THE MAIN REFERENCE FOR THIS ENTRY, TABLE 3.

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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
D: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
L: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2958
Polymers147,4384
Non-polymers1,8574
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19670 Å2
ΔGint-128 kcal/mol
Surface area44110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.400, 108.672, 196.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological active unit is the tetramer. Crystal contains four chains (A,D,H,L) and four molecules of the inhibitors (compound here labeled 870 in the asymmetric unit. The biological unit is the same of the other two related entries: 2fhy, 2fie

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Components

#1: Protein
Fructose-1,6-bisphosphatase 1


Mass: 36859.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: liver / Plasmid: 6His-Xpress-huFBP1-pET100-D-TOPO / Production host: Escherichia coli (E. coli)
References: GenBank: 15277851, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: Chemical
ChemComp-870 / N-[7-(3-AMINOPHENYL)-5-METHOXY-1,3-BENZOXAZOL-2-YL]-2,5-DICHLOROBENZENESULFONAMIDE


Mass: 464.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H15Cl2N3O4S

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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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, under oil / pH: 6.5
Details: Crystals grown under oil (3:1 parafin:silicon oil). 2 uL+2uL drops. Well solution: 14-18% PEG1000, 0.1 M Tris pH 8.0 Cryo: quick immersion in: 16% PEG1000, 20% PEG400,0.1 M Tris pH 8.0, pH 6. ...Details: Crystals grown under oil (3:1 parafin:silicon oil). 2 uL+2uL drops. Well solution: 14-18% PEG1000, 0.1 M Tris pH 8.0 Cryo: quick immersion in: 16% PEG1000, 20% PEG400,0.1 M Tris pH 8.0, pH 6.5, vapor diffusion, under oil, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 27761 / Num. obs: 23224 / % possible obs: 88.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.245 / Rsym value: 0.245 / Net I/σ(I): 3.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 0.69 / Num. unique all: 1651 / Rsym value: 0.88 / % possible all: 60.7

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Processing

Software
NameVersionClassification
CNX2002refinement
MAR345data collection
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: entry 2fie

2fie


Resolution: 3.5→19.88 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 73686.99 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2
Details: Entries 2fhy, 2fie and 2fix characterize the binding mode of benzoxazoles as allosteric inhibitors of human liver FBPase as described in the associated references. These three entries focus ...Details: Entries 2fhy, 2fie and 2fix characterize the binding mode of benzoxazoles as allosteric inhibitors of human liver FBPase as described in the associated references. These three entries focus on the binding mode and interactions in the proximity of the ligands. The medium to low resolution of the crystallographic data (3.3, 2.95 and 2.8 A) and the limited quality and extent of the available data, especially for entry 2fix, should be considered when trying to extract accurate interatomic distances between the ligands and the protein, at certain regions of the protein exposed to solvent.
RfactorNum. reflection% reflectionSelection details
Rfree0.355 1485 10.3 %RANDOM
Rwork0.252 ---
all0.307 18885 --
obs-14374 61.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.171068 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--17.2 Å20 Å20 Å2
2---5.05 Å20 Å2
3---22.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.45 Å
Luzzati d res low-8 Å
Luzzati sigma a0.61 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.5→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9728 0 120 0 9848
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.66 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.386 107 10.5 %
Rwork0.288 908 -
obs-908 35.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ACCELRYS_CNX_TOPPAR:protein_rep.paramprotein.top
X-RAY DIFFRACTION2ACCELRYS_CNX_TOPPAR:water_rep.paramion.top
X-RAY DIFFRACTION3ACCELRYS_CNX_TOPPAR:ion.param870.top
X-RAY DIFFRACTION4870.par

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