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- PDB-7wjv: Crystal structure of human liver FBPase complexed with an covalen... -

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Basic information

Entry
Database: PDB / ID: 7wjv
TitleCrystal structure of human liver FBPase complexed with an covalent inhibitor
ComponentsFructose-1,6-bisphosphatase 1
KeywordsCYTOSOLIC PROTEIN / Classification: HYDROLASE Organism(s): Homo sapiens Expression System: Escherichia coli BL21(DE3) inhibitor: covalent binding C128
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE / benzylcarbamic acid / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.724 Å
AuthorsCao, H. / Huang, Y. / Ren, Y. / Wan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177036 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: N -Acylamino Saccharin as an Emerging Cysteine-Directed Covalent Warhead and Its Application in the Identification of Novel FBPase Inhibitors toward Glucose Reduction.
Authors: Wen, W. / Cao, H. / Xu, Y. / Ren, Y. / Rao, L. / Shao, X. / Chen, H. / Wu, L. / Liu, J. / Su, C. / Peng, C. / Huang, Y. / Wan, J.
History
DepositionJan 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,87615
Polymers152,8274
Non-polymers2,04811
Water20,8611158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19600 Å2
ΔGint-113 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.641, 83.617, 278.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Fructose-1,6-bisphosphatase 1 / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6- ...Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA


Mass: 38206.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2TU34

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Non-polymers , 6 types, 1169 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-LSA / 1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE / SACCHARIN


Mass: 183.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PMQ / benzylcarbamic acid


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1158 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 0.1 M Tris (pH 6.8), 14% (v/v) EtOH, 7.5mM AMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.72→46.453 Å / Num. obs: 167125 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.992 / Net I/σ(I): 8.5
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 7923 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zwk

5zwk


Resolution: 1.724→46.453 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 2000 1.2 %
Rwork0.1743 164992 -
obs0.1746 166992 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.25 Å2 / Biso mean: 23.8414 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: final / Resolution: 1.724→46.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9868 0 134 1158 11160
Biso mean--26.01 34.28 -
Num. residues----1295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7243-1.76740.29461390.25581143998
1.7674-1.81520.291410.232211666100
1.8152-1.86860.27571410.211311643100
1.8686-1.92890.25781420.193111709100
1.9289-1.99790.19511420.177311696100
1.9979-2.07780.18571420.176311689100
2.0778-2.17240.19971420.175111747100
2.1724-2.28690.20871420.173511744100
2.2869-2.43020.181430.166511770100
2.4302-2.61780.18671430.175311796100
2.6178-2.88130.21121430.175411824100
2.8813-3.29810.21211440.167311857100
3.2981-4.15480.17171460.154912020100
4.1548-46.4530.17751500.170912392100

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