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

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Basic information

Entry
Database: PDB / ID: 5pzv
TitleHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(4-bromopyridin-2-yl)-3-(4-chlorophenyl)sulfonylurea
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
Chem-94G / 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 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 1-(4-bromopyridin-2-yl)-3-(4-chlorophenyl)sulfonylurea
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 11, 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)149,0008
Polymers147,4384
Non-polymers1,5634
Water18,0511002
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15960 Å2
ΔGint-75 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.618, 83.409, 277.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 61 or resid 72 through 335))
21chain B
31(chain C and (resid 9 through 61 or resid 72 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
11ASPASPGLYGLY(chain A and (resid 9 through 61 or resid 72 through 335))AA9 - 6110 - 62
12LYSLYSSERSER(chain A and (resid 9 through 61 or resid 72 through 335))AA72 - 33573 - 336
21ASPASPSERSERchain BBB9 - 33510 - 336
31ASPASPGLYGLY(chain C and (resid 9 through 61 or resid 72 through 335))CC9 - 6110 - 62
32LYSLYSSERSER(chain C and (resid 9 through 61 or resid 72 through 335))CC72 - 33573 - 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-94G / N-[(4-bromopyridin-2-yl)carbamoyl]-4-chlorobenzene-1-sulfonamide


Mass: 390.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H9BrClN3O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1002 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12% 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: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→29.672 Å / Num. obs: 100175 / % possible obs: 93.75 %

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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→29.672 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 5009 5 %
Rwork0.1906 95166 -
obs0.193 100175 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.9 Å2 / Biso mean: 29.6444 Å2 / Biso min: 5.02 Å2
Refinement stepCycle: final / Resolution: 2→29.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9729 0 84 1002 10815
Biso mean--56.99 37.29 -
Num. residues----1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079989
X-RAY DIFFRACTIONf_angle_d0.9113496
X-RAY DIFFRACTIONf_chiral_restr0.0571528
X-RAY DIFFRACTIONf_plane_restr0.0061723
X-RAY DIFFRACTIONf_dihedral_angle_d10.4496062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6090X-RAY DIFFRACTION9.362TORSIONAL
12B6090X-RAY DIFFRACTION9.362TORSIONAL
13C6090X-RAY DIFFRACTION9.362TORSIONAL
14D6090X-RAY DIFFRACTION9.362TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.34331740.27052899307387
2.0227-2.04650.32511570.25222851300885
2.0465-2.07150.31491430.25532896303987
2.0715-2.09770.31841530.2492917307087
2.0977-2.12530.3361850.2452903308888
2.1253-2.15440.30221490.22952957310688
2.1544-2.18520.25611410.22472983312488
2.1852-2.21780.3231340.22512984311889
2.2178-2.25240.29631780.21982942312088
2.2524-2.28930.26021550.21242977313290
2.2893-2.32880.23931530.20453032318589
2.3288-2.37110.29141470.20153032317991
2.3711-2.41670.25541800.1943013319390
2.4167-2.4660.27091560.19813080323692
2.466-2.51960.25071570.20273111326892
2.5196-2.57820.25031800.20383102328294
2.5782-2.64260.2591610.20253204336595
2.6426-2.7140.24121590.20223235339496
2.714-2.79380.24511650.1953310347598
2.7938-2.88390.25491980.19293320351899
2.8839-2.98690.24191790.195833853564100
2.9869-3.10640.24081650.198233773542100
3.1064-3.24760.2281590.190634313590100
3.2476-3.41860.23582020.180433383540100
3.4186-3.63240.2221840.169934193603100
3.6324-3.91230.22061770.166834263603100
3.9123-4.30490.18151820.162634443626100
4.3049-4.92540.17371910.146634363627100
4.9254-6.19620.22111740.177335143688100
6.1962-29.6750.22481710.19023648381999
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)
10.04270.00980.00430.017-0.03120.042-0.08140.0802-0.00940.03110.13760.0137-0.0409-0.02570.00130.17450.01190.03570.15380.00960.133217.067641.873216.0126
20.03430.0154-0.02940.0633-0.05850.0596-0.03880.11970.0775-0.00520.0072-0.0204-0.12540.0709-0.06360.116-0.06360.04160.17960.01250.109334.719944.622610.9063
30.0142-0.0173-0.0040.00320.0010.00640.04760.0638-0.0004-0.0546-0.002-0.0998-0.07320.117600.216-0.05870.06260.25840.00160.161736.939345.58252.834
40.0355-0.02420.01610.01790.00830.01320.0034-0.029-0.04030.08450.03360.0376-0.01550.060.00190.09620.00760.0130.1302-0.03180.14636.562319.252937.2165
50.0588-0.0293-0.02650.0562-0.00390.00870.09840.1318-0.13690.00710.03620.0328-0.05880.15740.17370.1236-0.00340.08040.2384-0.11230.084341.613918.521818.9496
60.01160.01780.00820.03130.00250.0334-0.06830.0649-0.0968-0.0175-0.0604-0.0403-0.01780.1191-0.10660.11380.08750.08120.3023-0.16270.04349.660916.330816.4007
70.0247-0.01290.00950.0590.03150.0175-0.007-0.01390.0387-0.10090.0356-0.0522-0.0396-0.0056-0.01320.12520.00430.04020.0574-0.02230.089916.184648.863441.5068
80.0402-0.0304-0.00880.0624-0.02690.04550.0027-0.02260.05770.0218-0.00460.086-0.0026-0.0642-0.02390.11290.0340.050.0916-0.01360.1169-2.746646.867949.6561
90.030.0264-0.01420.0278-0.03580.0259-0.01580.0578-0.1076-0.05150.0455-0.01930.0571-0.01520.00750.12470.01570.01460.0768-0.02010.130812.226512.734637.0258
100.15140.0647-0.06430.0739-0.02410.07580.0491-0.0214-0.0770.1085-0.0276-0.01860.0422-0.00090.0730.1156-0.00640.05610.06730.01590.05982.597417.111455.3823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 131 )A9 - 131
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 247 )A132 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 335 )A248 - 335
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 122 )B9 - 122
5X-RAY DIFFRACTION5chain 'B' and (resid 123 through 247 )B123 - 247
6X-RAY DIFFRACTION6chain 'B' and (resid 248 through 335 )B248 - 335
7X-RAY DIFFRACTION7chain 'C' and (resid 9 through 131 )C9 - 131
8X-RAY DIFFRACTION8chain 'C' and (resid 132 through 335 )C132 - 335
9X-RAY DIFFRACTION9chain 'D' and (resid 9 through 122 )D9 - 122
10X-RAY DIFFRACTION10chain 'D' and (resid 123 through 335 )D123 - 335

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