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- PDB-5pzq: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

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Basic information

Entry
Database: PDB / ID: 5pzq
TitleHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 2-(4-methoxyphenyl)furan-3,4-dicarboxylic acid
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE/HYDROLASE inhibitor / D3R docking / HYDROLASE-HYDROLASE inhibitor complex
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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / Gluconeogenesis / 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
2-(4-methoxyphenyl)furan-3,4-dicarboxylic acid / Fructose-1,6-bisphosphatase 1 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
Model detailsFor D3R project
AuthorsRuf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: To be published
Title: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 2-(4-methoxyphenyl)furan-3,4-dicarboxylic acid
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 10, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,4878
Polymers147,4384
Non-polymers1,0494
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-93 kcal/mol
Surface area44390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.950, 143.400, 74.220
Angle α, β, γ (deg.)90.000, 108.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 71 or resid 73 through 335))
21chain B
31(chain C and (resid 9 through 71 or resid 73 through 335))
41chain D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYS(chain A and (resid 9 through 71 or resid 73 through 335))AA9 - 7110 - 72
12LEULEUSERSER(chain A and (resid 9 through 71 or resid 73 through 335))AA73 - 33574 - 336
21ASPASPSERSERchain BBB9 - 33510 - 336
31ASPASPLYSLYS(chain C and (resid 9 through 71 or resid 73 through 335))CC9 - 7110 - 72
32LEULEUSERSER(chain C and (resid 9 through 71 or resid 73 through 335))CC73 - 33574 - 336
41ASPASPSERSERchain DDD9 - 33510 - 336

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Components

#1: Protein
Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / 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: 36859.418 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 (E. coli)
References: UniProt: Q2TU34, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: Chemical
ChemComp-93V / 2-(4-methoxyphenyl)furan-3,4-dicarboxylic acid


Mass: 262.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H10O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12%-25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.7→41.277 Å / Num. obs: 36412 / % possible obs: 99.69 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.23data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.277 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.57 / Stereochemistry target values: ML / Details: INHIBITOR IN SUBUNIT D ONLY WEAKLY BOUND
RfactorNum. reflection% reflection
Rfree0.2333 1820 5 %
Rwork0.1624 34592 -
obs0.166 36412 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.88 Å2 / Biso mean: 52.9733 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 2.7→41.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9722 0 76 97 9895
Biso mean--63.87 41.36 -
Num. residues----1270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089974
X-RAY DIFFRACTIONf_angle_d1.01513474
X-RAY DIFFRACTIONf_chiral_restr0.0591526
X-RAY DIFFRACTIONf_plane_restr0.0061726
X-RAY DIFFRACTIONf_dihedral_angle_d10.9756062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6104X-RAY DIFFRACTION11.969TORSIONAL
12B6104X-RAY DIFFRACTION11.969TORSIONAL
13C6104X-RAY DIFFRACTION11.969TORSIONAL
14D6104X-RAY DIFFRACTION11.969TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.7730.35351390.23522607274698
2.773-2.85460.30141470.211726552802100
2.8546-2.94670.33531290.21126622791100
2.9467-3.0520.29161280.20126812809100
3.052-3.17410.29231460.188826562802100
3.1741-3.31850.24271420.172926562798100
3.3185-3.49340.24091230.168226632786100
3.4934-3.71220.23861400.161726742814100
3.7122-3.99860.22491290.151426692798100
3.9986-4.40050.2111510.132826602811100
4.4005-5.03640.18091330.120826642797100
5.0364-6.34160.21321500.162126732823100
6.3416-41.28180.20711630.16452672283599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0546-0.09650.05470.2147-0.10670.0599-0.0368-0.0574-0.0920.01540.12220.0724-0.0877-0.04040.02250.134-0.0393-0.03590.21150.00810.1213-6.6437-0.980734.1219
20.0487-0.0426-0.01430.04610.01660.00130.01080.02260.07460.08990.06730.1128-0.1091-0.12690.04020.17490.0574-0.03480.22380.0420.2259-10.802816.916129.6873
30.04050.0009-0.05550.0206-0.03560.11520.0009-0.02530.04750.07620.09950.0851-0.0932-0.18570.15370.14110.1623-0.00070.25230.10610.2811-19.175820.088229.9341
40.0251-0.0036-0.00170.0497-0.01130.00840.00840.11560.1011-0.0383-0.0266-0.09820.1405-0.03580.00170.2759-0.04160.0080.28960.06490.235317.673314.4210.8367
50.0288-0.00410.04910.0286-0.01620.07310.05280.21670.066-0.1036-0.0597-0.04210.0449-0.00430.00740.282-0.0084-0.02710.33120.07830.14958.07914.29212.791
60.00420.0008-0.00890.0208-0.01350.04360.08480.12370.0701-0.0652-0.03250.0664-0.044-0.14410.07040.29220.2504-0.10660.43670.26760.1654-5.225226.25352.3119
70.0296-0.02460.00470.028-0.02090.0147-0.0808-0.11440.07210.02410.02650.0060.0301-0.05380.00090.1672-0.0156-0.04730.23770.01870.115116.9064-0.078344.6836
80.1077-0.02630.03940.18770.00220.0157-0.0457-0.2304-0.16030.06760.0592-0.09950.0193-0.03290.0340.17210.004-0.01650.25130.10760.265718.1819-12.462944.7953
90.0258-0.02730.00930.0268-0.01020.0017-0.0734-0.061-0.05710.0403-0.0251-0.09080.02260.0474-0.13390.11430.1171-0.02550.11820.13740.393932.9479-27.30641.135
100.03390.0202-0.0140.009-0.00670.0436-0.033-0.0629-0.07390.07830.0133-0.03070.03470.0486-0.00550.35780.0017-0.0840.31190.3030.405727.6482-22.079752.1325
110.1009-0.05350.04920.0562-0.00760.04020.02250.1527-0.1124-0.13140.03230.0042-0.01980.0430.12430.3013-0.16080.05080.1995-0.12120.140618.549-11.53938.3828
120.0273-0.01720.00540.0161-0.00480.02360.02820.0682-0.0632-0.06570.0215-0.0566-0.00240.01590.07740.3121-0.04790.12460.1818-0.17690.185927.287-16.8439.2316
130.02730.02790.01760.05430.03290.0194-0.05970.0114-0.1378-0.06130.0563-0.08880.04830.05190.00540.1183-0.00510.04690.11150.00190.280733.9375-7.179620.1828
140.0021-0.0037-0.00190.00490.00190.0003-0.00010.0132-0.00540.00070.0066-0.00620.03660.010400.41570.12290.03610.30860.11240.662842.6807-32.388628.464
150.0141-0.00310.0070.03550.00270.0175-0.0047-0.0109-0.02550.01720.02330.02680.06740.03750.01490.17390.07880.02230.12760.03140.342838.4652-23.16525.9327
160.01890.013-0.02230.02060.00350.0603-0.0537-0.0066-0.05560.00830.0019-0.05960.08610.0338-0.08310.19140.06990.17880.0722-0.07210.381639.6314-24.984713.4962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 122 )A9 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 247 )A123 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 335 )A248 - 335
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 131 )B9 - 131
5X-RAY DIFFRACTION5chain 'B' and (resid 132 through 212 )B132 - 212
6X-RAY DIFFRACTION6chain 'B' and (resid 213 through 335 )B213 - 335
7X-RAY DIFFRACTION7chain 'C' and (resid 9 through 122 )C9 - 122
8X-RAY DIFFRACTION8chain 'C' and (resid 123 through 212 )C123 - 212
9X-RAY DIFFRACTION9chain 'C' and (resid 213 through 274 )C213 - 274
10X-RAY DIFFRACTION10chain 'C' and (resid 275 through 335 )C275 - 335
11X-RAY DIFFRACTION11chain 'D' and (resid 9 through 122 )D9 - 122
12X-RAY DIFFRACTION12chain 'D' and (resid 123 through 179 )D123 - 179
13X-RAY DIFFRACTION13chain 'D' and (resid 180 through 212 )D180 - 212
14X-RAY DIFFRACTION14chain 'D' and (resid 213 through 231 )D213 - 231
15X-RAY DIFFRACTION15chain 'D' and (resid 232 through 274 )D232 - 274
16X-RAY DIFFRACTION16chain 'D' and (resid 275 through 335 )D275 - 335

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