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- PDB-8xbk: Crystal Structure of Human Liver Fructose-1,6-bisphosphatase Comp... -

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Basic information

Entry
Database: PDB / ID: 8xbk
TitleCrystal Structure of Human Liver Fructose-1,6-bisphosphatase Complexed with a Covalent Inhibitor
ComponentsFructose-1,6-bisphosphatase 1
KeywordsPROTEIN BINDING / covalent inhibitor
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
: / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsCao, H. / Zhang, X. / Ren, Y. / Wan, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177036 China
National Natural Science Foundation of China (NSFC)21873035 China
National Natural Science Foundation of China (NSFC)22377030 China
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure-Guided Design of Affinity/Covalent-Bond Dual-Driven Inhibitors Targeting the AMP Site of FBPase
Authors: Cao, H. / Huang, Z. / Liu, Z. / Zhang, X. / Ren, Y. / Hameed, M.S. / Rao, L. / Makunga, N.P. / Dobrikov, G.M. / Wan, J.
History
DepositionDec 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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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)155,77929
Polymers152,8274
Non-polymers2,95125
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19520 Å2
ΔGint-63 kcal/mol
Surface area43460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.115, 82.950, 275.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical
ChemComp-YR9 / N-[2-[4-[(3-bromophenyl)carbamoylsulfamoyl]phenyl]ethyl]ethanamide


Mass: 440.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18BrN3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris (pH 8.8), 15% (v/v) EtOH, 5mM CW7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.42→48.8 Å / Num. obs: 58044 / % possible obs: 97.55 % / Redundancy: 12.8 % / CC1/2: 0.999 / Net I/σ(I): 17.52
Reflection shellResolution: 2.425→2.511 Å / Rmerge(I) obs: 0.6596 / Mean I/σ(I) obs: 3.14 / Num. unique obs: 5202 / CC1/2: 0.857

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→48.8 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2903 5 %
Rwork0.1826 --
obs0.1852 58038 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9822 0 179 306 10307
Refine LS restraintsType: f_chiral_restr / Dev ideal: 0.054 / Number: 1547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.460.3051160.23122201X-RAY DIFFRACTION84
2.46-2.510.28311320.21952498X-RAY DIFFRACTION94
2.51-2.550.30411330.21892537X-RAY DIFFRACTION96
2.55-2.60.30921380.20852612X-RAY DIFFRACTION97
2.6-2.650.26791360.20432586X-RAY DIFFRACTION99
2.65-2.710.28621380.20532623X-RAY DIFFRACTION99
2.71-2.780.28991370.20472594X-RAY DIFFRACTION98
2.78-2.850.30411360.21722600X-RAY DIFFRACTION99
2.85-2.920.30391410.21462671X-RAY DIFFRACTION99
2.92-3.010.29531360.21112594X-RAY DIFFRACTION98
3.01-3.10.25571390.20762637X-RAY DIFFRACTION98
3.11-3.220.29261400.19462655X-RAY DIFFRACTION99
3.22-3.340.24611400.1892655X-RAY DIFFRACTION99
3.34-3.50.2631380.20162628X-RAY DIFFRACTION99
3.5-3.680.24011410.18052678X-RAY DIFFRACTION99
3.68-3.910.23021410.17192674X-RAY DIFFRACTION99
3.91-4.210.22741410.172678X-RAY DIFFRACTION99
4.21-4.640.17891410.14362689X-RAY DIFFRACTION99
4.64-5.310.19951430.14682716X-RAY DIFFRACTION99
5.31-6.680.22531450.18832745X-RAY DIFFRACTION99

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