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- PDB-6ls5: Structure of human liver FBPase complexed with covalent allosteri... -

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Basic information

Entry
Database: PDB / ID: 6ls5
TitleStructure of human liver FBPase complexed with covalent allosteric inhibitor
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / FBPase
Function / homology
Function and homology information


cellular response to raffinose / cellular hypotonic salinity response / fructose-bisphosphatase / cellular response to phorbol 13-acetate 12-myristate / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / Gluconeogenesis / fructose metabolic process ...cellular response to raffinose / cellular hypotonic salinity response / fructose-bisphosphatase / cellular response to phorbol 13-acetate 12-myristate / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / cellular hyperosmotic salinity response / AMP binding / cellular response to cAMP / gluconeogenesis / response to nutrient levels / negative regulation of cell growth / cellular response to xenobiotic stimulus / cellular response to insulin stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / identical protein binding / nucleus / cytoplasm / 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 / 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 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 / 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
ADENOSINE MONOPHOSPHATE / 2-(ethyldisulfanyl)-1,3-benzothiazole / Fructose-1,6-bisphosphatase 1 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.031 Å
AuthorsYunyuan, H. / Rongrong, S. / Yixiang, X. / Shuaishuai, N. / Yanliang, R. / Jian, L. / Jian, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21877046, 21873035, 21572077 and 21472061 China
CitationJournal: J.Med.Chem. / Year: 2020
Title: Identification of the New Covalent Allosteric Binding Site of Fructose-1,6-bisphosphatase with Disulfiram Derivatives toward Glucose Reduction.
Authors: Huang, Y. / Xu, Y. / Song, R. / Ni, S. / Liu, J. / Xu, Y. / Ren, Y. / Rao, L. / Wang, Y. / Wei, L. / Feng, L. / Su, C. / Peng, C. / Li, J. / Wan, J.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.4Nov 6, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,82013
Polymers155,1064
Non-polymers1,7139
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-134 kcal/mol
Surface area44380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.599, 83.523, 276.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 38776.508 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, UniProt: P09467*PLUS
#2: Chemical ChemComp-EUF / 2-(ethyldisulfanyl)-1,3-benzothiazole


Mass: 227.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NS3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05 M Tris (pH 6.8), 10% (v/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.06 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.031→42.842 Å / Num. obs: 1353784 / % possible obs: 99.7 % / Redundancy: 8.4 % / CC1/2: 0.996 / Net I/σ(I): 11.34
Reflection shellResolution: 2.031→2.041 Å / Mean I/σ(I) obs: 2.29 / Num. unique obs: 12417 / CC1/2: 0.765

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZWK

5zwk


Resolution: 2.031→42.842 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 5092 5 %
Rwork0.1942 96759 -
obs0.1963 101851 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.4 Å2 / Biso mean: 33.0536 Å2 / Biso min: 16.11 Å2
Refinement stepCycle: final / Resolution: 2.031→42.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9912 0 99 640 10651
Biso mean--41.91 37.5 -
Num. residues----1297
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.031-2.05380.31841570.252298294
2.0538-2.0780.26841670.23363179100
2.078-2.10330.26471690.22773208100
2.1033-2.12990.29951670.22223172100
2.1299-2.1580.27711690.21513208100
2.158-2.18750.26621690.21253220100
2.1875-2.21880.26211670.2183165100
2.2188-2.25190.30841700.25213225100
2.2519-2.28710.30531670.24213177100
2.2871-2.32460.28561690.21433221100
2.3246-2.36460.23871670.20473166100
2.3646-2.40760.26581700.20253222100
2.4076-2.45390.2591680.20573204100
2.4539-2.5040.28471700.21223227100
2.504-2.55850.25851680.21473190100
2.5585-2.6180.28131700.2162322799
2.618-2.68340.25991680.20383201100
2.6834-2.7560.26551680.21033198100
2.756-2.83710.27491700.20383232100
2.8371-2.92860.23411690.20323210100
2.9286-3.03330.25261700.20293234100
3.0333-3.15470.26731710.19953245100
3.1547-3.29820.22541700.19323239100
3.2982-3.4720.24061720.18823267100
3.472-3.68940.20651710.18123244100
3.6894-3.97410.21121730.1774328499
3.9741-4.37370.21081710.16983252100
4.3737-5.00570.1841740.15643303100
5.0057-6.30350.221760.18623360100
6.3035-42.8420.20331850.1851349799

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