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- PDB-5q05: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

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Basic information

Entry
Database: PDB / ID: 5q05
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-(5-bromo-1,3-thiazol-2-yl)-3-[5-(2-methoxyethyl)-4-methylthiophen-2-yl]sulfonylurea
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHydrolase/Hydrolase Inhibitor / D3R docking / Hydrolase-Hydrolase Inhibitor complex
Function / homologyFructose-1,6-bisphosphatase class 1 / Fructose-1,6-bisphosphatase, active site / Fructose-1,6-bisphosphatase / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase active site. / fructose 1,6-bisphosphate 1-phosphatase activity / carbohydrate metabolic process / Fructose-1,6-bisphosphatase 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2.2 Å resolution
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-(5-bromo-1,3-thiazol-2-yl)-3-[5-(2-methoxyethyl)-4-methylthiophen-2-yl]sulfonylurea
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 20, 2017 / Release: Jan 9, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 9, 2019Structure modelrepositoryInitial release
1.1Jan 16, 2019Structure modelData collectiondiffrn_radiation_diffrn_radiation.pdbx_diffrn_protocol
1.2Feb 6, 2019Structure modelData collection / Database references / Structure summaryaudit_author / citation_author_audit_author.name / _citation_author.name

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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
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,39816
Polyers294,8758
Non-polymers3,5238
Water16,322906
1
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)149,1998
Polyers147,4384
Non-polymers1,7614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15760
ΔGint (kcal/M)-84
Surface area (Å2)44520
MethodPISA
2
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1998
Polyers147,4384
Non-polymers1,7614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15730
ΔGint (kcal/M)-83
Surface area (Å2)44330
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)66.728, 285.434, 83.912
Angle α, β, γ (deg.)90.000, 97.470, 90.000
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide
Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / 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.: 8 / Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TU34, fructose-bisphosphatase
#2: Chemical
ChemComp-95S / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-5-(2-methoxyethyl)-4-methylthiophene-2-sulfonamide


Mass: 440.356 Da / Num. of mol.: 8 / Formula: C12H14BrN3O4S3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 906 / Formula: H2O / Water

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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: 2.78 / Density percent sol: 55.68 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Collection date: Aug 17, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionD resolution high: 2.2 Å / D resolution low: 29.12 Å / Number obs: 150662 / Percent possible obs: 96.14

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationContact authorContact author emailDateLanguageLocationType
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.23data extractionPDBdeposit[at]deposit.rcsb.orgDec. 13, 2016C++http://sw-tools.pdb.org/apps/PDB_EXTRACT/package
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.3 / Cross valid method: THROUGHOUT / Sigma F: 1.38 / Overall phase error: 25.02 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 159.57 Å2 / B iso mean: 43.7966 Å2 / B iso min: 10.63 Å2
Least-squares processR factor R free: 0.2396 / R factor R work: 0.1869 / R factor obs: 0.1896 / Highest resolution: 2.2 Å / Lowest resolution: 29.12 Å / Number reflection R free: 7552 / Number reflection R work: 143110 / Number reflection obs: 150662 / Percent reflection R free: 5.01 / Percent reflection obs: 96.14
Refine hist #finalHighest resolution: 2.2 Å / Lowest resolution: 29.12 Å / B iso mean ligand: 43.49 / B iso mean solvent: 43.92 / Number residues total: 2540
Number of atoms included #finalProtein: 19440 / Nucleic acid: 0 / Ligand: 184 / Solvent: 906 / Total: 20530
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820009
X-RAY DIFFRACTIONf_angle_d0.96027033
X-RAY DIFFRACTIONf_chiral_restr0.0593054
X-RAY DIFFRACTIONf_plane_restr0.0063450
X-RAY DIFFRACTIONf_dihedral_angle_d11.11612161
Refine LS restraints ncs

Ens ID: 1 / Number: 12225 / Refine ID: X-RAY DIFFRACTION / Rms: 9.72 / Type: TORSIONAL

Dom IDAuth asym ID
1A
2B
3C
4D
5E
6F
7G
8H
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.20000.33530.29852.22501342885301957.0000
2.22500.35520.29202.25121973679387675.0000
2.25120.35310.27242.27862154059427481.0000
2.27860.33490.25432.30742274232445986.0000
2.30740.31190.24252.33782574474473191.0000
2.33780.29030.22512.36982484793504197.0000
2.36980.30120.21302.403626849585226100.0000
2.40360.28860.21122.439525749445201100.0000
2.43950.28640.22012.477626750105277100.0000
2.47760.29970.20952.518225049055155100.0000
2.51820.27580.20772.561628349805263100.0000
2.56160.28270.21372.608127049065176100.0000
2.60810.27790.21452.658325649715227100.0000
2.65830.29940.21472.712525649555211100.0000
2.71250.29220.20522.771423750065243100.0000
2.77140.25330.19092.835824449195163100.0000
2.83580.25110.20072.906730249895291100.0000
2.90670.27210.19772.985227849045182100.0000
2.98520.24550.19243.073025149615212100.0000
3.07300.26200.18903.172024050025242100.0000
3.17200.21630.18773.285323549535188100.0000
3.28530.25670.19053.416626549305195100.0000
3.41660.22880.18253.571824550055250100.0000
3.57180.22390.17513.759828549595244100.0000
3.75980.21590.16593.994827549635238100.0000
3.99480.21100.16274.302325749175174100.0000
4.30230.18760.15624.733628249825264100.0000
4.73360.19670.15775.414824049635203100.0000
5.41480.21370.17466.807726649715237100.0000
6.80770.19710.163529.12262654935520098.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.17930.0181-0.03950.1235-0.18640.1783-0.0311-0.01310.0316-0.1844-0.0801-0.0749-0.05630.02560.00020.29560.01440.02040.17910.01450.208437.969816.1515-5.3626
20.3359-0.19240.04300.2908-0.13880.2769-0.01350.01560.0059-0.1652-0.03980.1142-0.07460.0553-0.00700.34620.0258-0.05210.1698-0.00280.240820.357923.0044-7.7372
30.2364-0.1298-0.08760.2548-0.04880.07880.1076-0.02200.1687-0.23560.06610.0282-0.03530.01530.47460.41720.1637-0.1852-0.07700.15330.177618.680331.4919-10.0836
40.2515-0.2258-0.16670.50490.01150.1310-0.0476-0.0059-0.0941-0.0344-0.00250.11940.04180.0309-0.03170.10920.00770.03040.22950.02500.262712.9580-2.815416.0259
50.1952-0.14930.03930.1908-0.10330.28630.0131-0.0510-0.04820.0004-0.00220.0872-0.05970.0749-0.00160.13250.03520.02560.1491-0.00240.18699.457915.698616.3499
60.0037-0.0325-0.04820.08740.11870.8426-0.0746-0.0345-0.1035-0.00310.14350.2272-0.3361-0.0066-0.00950.13480.09490.04240.22630.01180.36091.352419.123217.7890
70.0082-0.0112-0.00590.01130.00430.0015-0.07270.07480.0776-0.1463-0.0098-0.1452-0.1282-0.06370.00000.40750.02380.07360.31190.02100.276147.72966.2330-14.6401
8-0.00860.0006-0.02520.02880.01250.06250.03310.0588-0.1065-0.1261-0.03250.16280.0898-0.06050.00000.20160.04650.02610.22600.00420.205831.5464-9.2939-6.6660
90.09740.0097-0.02240.08960.08250.0789-0.01340.0736-0.05560.10170.00490.11550.1248-0.03020.00000.27200.08550.00130.2532-0.01200.231436.7253-16.0075-15.0577
100.04750.0401-0.13100.0277-0.09620.29050.05400.1036-0.0509-0.0680-0.14150.01970.0943-0.0714-0.29760.26340.09060.10940.21020.07400.028243.4071-13.8012-22.7700
110.04010.00930.00400.03460.00450.00710.0785-0.0175-0.0238-0.1961-0.11990.0115-0.00670.0869-0.00000.27510.03580.05560.23800.01790.174847.1034-14.2406-14.9755
120.07920.00950.04340.03470.05920.1065-0.07450.0528-0.0232-0.16440.0809-0.0471-0.12910.0618-0.00700.17500.00110.06730.25590.02470.240151.8831-6.2208-2.5918
130.07240.0242-0.09870.0574-0.00700.1223-0.25670.0917-0.0801-0.1032-0.0499-0.06070.0846-0.0005-0.00420.27390.08250.01430.26380.03100.326961.8263-28.90704.2417
140.0325-0.00430.0207-0.0003-0.00930.10650.05960.0437-0.1221-0.1686-0.0642-0.05060.1305-0.0046-0.00000.25860.01300.01740.20320.01090.229052.0771-21.0638-6.3062
150.0632-0.0655-0.02770.0639-0.00080.05660.10020.1455-0.0268-0.2162-0.0951-0.12810.14110.1270-0.04720.26390.07560.10080.2870-0.00920.243459.9040-24.6852-11.2147
160.0289-0.1248-0.03130.2407-0.01620.23320.0939-0.03080.15740.13980.02180.0542-0.0405-0.07030.13480.17950.03720.05640.24470.02340.185436.2579-4.881825.3083
170.2099-0.1258-0.11060.3256-0.25710.3364-0.0003-0.0771-0.03150.0570-0.0235-0.05810.08100.0619-0.09500.14370.04240.00790.16750.02470.169844.5920-24.064321.9575
180.02300.0045-0.03380.0114-0.01550.04090.0111-0.12700.22070.1948-0.08230.0481-0.01220.13130.00010.4656-0.04270.01940.2855-0.00980.2575-8.044460.141557.3727
190.01490.0095-0.00340.0013-0.00240.00860.1223-0.0142-0.14530.0934-0.06250.2109-0.09420.17400.00010.2698-0.0026-0.05560.1831-0.01070.2362-1.919153.896444.5036
200.03680.03800.02840.03610.02250.03230.07180.0177-0.05450.0464-0.0721-0.00930.10590.30460.00000.33160.0474-0.07410.24860.00610.24682.823051.250331.3627
210.00180.0085-0.00290.0180-0.01310.01340.08170.1358-0.2441-0.0268-0.0894-0.01190.05570.1767-0.00010.44330.0733-0.09130.31550.01190.42764.008439.089345.4726
220.1040-0.0935-0.07500.06180.05560.0523-0.14160.0019-0.21680.1898-0.00950.06350.10160.1107-0.00000.3945-0.0163-0.06490.32040.00450.3558-2.998244.200040.2137
230.16610.0132-0.10400.12150.17910.25530.0616-0.0448-0.04450.2429-0.13960.00120.0578-0.0895-0.00770.3022-0.06890.00200.17870.01830.2856-12.414047.654947.2379
240.02390.0192-0.02140.02170.01040.0369-0.0209-0.0486-0.09860.00310.0255-0.23590.0786-0.09440.00090.2942-0.09920.09800.3368-0.07600.5177-32.333434.981933.4745
250.12870.09090.08260.07070.00440.06530.03870.0115-0.15070.0301-0.05590.02240.2092-0.1003-0.00000.3775-0.09980.02750.2022-0.00270.4379-20.590835.537843.6922
260.17880.19760.03520.3248-0.10110.18690.00670.13870.0171-0.0790-0.01990.1567-0.14280.04670.03030.25560.0318-0.07140.2943-0.05080.2668-18.444469.614016.7328
270.3298-0.0926-0.23710.3306-0.12140.25160.02970.2193-0.06600.0055-0.10820.07820.0334-0.0018-0.04500.2012-0.0100-0.06210.2903-0.15390.2789-22.303651.083315.7524
280.0296-0.0112-0.00400.0498-0.02610.0966-0.11720.1541-0.1157-0.00790.09590.09640.0186-0.09740.02800.21520.0196-0.06420.3914-0.15750.3987-29.961347.908812.3428
290.0126-0.0095-0.01070.00200.00660.00570.05120.0667-0.15130.2569-0.0748-0.06630.05150.1083-0.00010.40990.0067-0.02440.22480.00950.23557.119259.805055.2907
300.09630.04750.00220.0070-0.01210.04250.0810-0.07870.07440.0376-0.06660.1076-0.0278-0.0823-0.00000.2816-0.0114-0.00290.16300.00140.1660-6.209375.695443.4911
310.10580.02710.04830.13220.09160.06610.0395-0.07900.1313-0.09300.05020.0871-0.04070.0096-0.00020.3177-0.07280.02880.26820.00970.2184-3.281682.263653.0233
320.01000.0165-0.00220.0149-0.01840.02930.1008-0.05940.00790.1831-0.1582-0.04540.13270.1065-0.00160.2005-0.0437-0.02460.2403-0.02680.20291.439479.607562.2577
330.2118-0.12750.04480.0849-0.04580.08760.0664-0.02380.00910.1339-0.0669-0.06500.09590.0182-0.00000.2651-0.0397-0.04400.21740.01910.192311.897974.929648.2269
340.0169-0.03520.04270.0793-0.08990.08910.0870-0.1348-0.0679-0.1833-0.18680.0270-0.18420.0491-0.00040.2339-0.0959-0.04970.36070.00130.295926.138994.805240.7462
350.0409-0.0134-0.0909-0.00130.02670.12840.0473-0.12960.05420.0484-0.10220.0307-0.25750.06500.00080.2228-0.0708-0.03690.21250.01150.204813.878887.108248.4625
360.18930.07790.03920.2860-0.10550.07820.0560-0.0451-0.07530.1706-0.09820.0682-0.18860.1088-0.03940.1878-0.1802-0.10180.2834-0.00440.193720.239990.605755.2049
370.0368-0.03130.00420.05700.04030.0695-0.18710.12490.05610.0841-0.10220.11320.1290-0.0794-0.00580.2991-0.0392-0.04580.49230.06720.3150-8.607279.80878.2720
380.01240.0018-0.04270.0116-0.04980.05960.06590.1163-0.1724-0.1059-0.0168-0.08440.31700.04230.00010.30390.0089-0.02220.26670.00340.19147.374667.142620.5260
390.03150.0244-0.02000.0158-0.00590.01910.15480.02990.05210.0138-0.0827-0.21420.2161-0.0415-0.00000.44690.08410.03990.3577-0.03000.230016.481070.34897.5428
400.01190.0140-0.00910.0127-0.00950.01580.0061-0.0396-0.1488-0.0952-0.0507-0.1325-0.0228-0.0345-0.00010.3937-0.0075-0.00180.31490.00140.209511.676572.74058.1889
410.09580.1000-0.05330.21610.01360.1144-0.0054-0.0452-0.1130-0.04220.0439-0.11200.14270.08840.03350.2572-0.00660.05590.25460.03420.142314.959477.954510.8142
420.0766-0.07120.00150.1558-0.03370.00250.04610.11750.0653-0.07270.00370.0596-0.01470.01180.00000.2116-0.0076-0.01180.22060.02780.13832.622486.097020.2265
430.0231-0.0079-0.02580.00330.00650.0207-0.0872-0.0791-0.0799-0.22630.0335-0.1392-0.2181-0.0095-0.00130.3093-0.09600.07020.31820.06330.309725.5345100.226428.7007
440.02450.0161-0.02000.0112-0.03160.07860.10930.12790.0490-0.00260.1066-0.1230-0.21260.03010.00090.2686-0.03650.04330.2433-0.02100.245516.645994.898726.9464
450.15550.13970.04510.09090.01880.09460.10210.0973-0.1106-0.0627-0.0185-0.08830.08220.05850.00010.3055-0.00590.06140.22670.01630.250717.922493.957414.6113
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A9A1221chain 'A' and (resid 9 through 122 )
2A123A2472chain 'A' and (resid 123 through 247 )
3A248A3353chain 'A' and (resid 248 through 335 )
4B9B1224chain 'B' and (resid 9 through 122 )
5B123B2475chain 'B' and (resid 123 through 247 )
6B248B3356chain 'B' and (resid 248 through 335 )
7C9C287chain 'C' and (resid 9 through 28 )
8C29C888chain 'C' and (resid 29 through 88 )
9C89C1319chain 'C' and (resid 89 through 131 )
10C132C14810chain 'C' and (resid 132 through 148 )
11C149C17011chain 'C' and (resid 149 through 170 )
12C171C21212chain 'C' and (resid 171 through 212 )
13C213C24713chain 'C' and (resid 213 through 247 )
14C248C29014chain 'C' and (resid 248 through 290 )
15C291C33515chain 'C' and (resid 291 through 335 )
16D9D12216chain 'D' and (resid 9 through 122 )
17D123D33517chain 'D' and (resid 123 through 335 )
18E9E2818chain 'E' and (resid 9 through 28 )
19E29E4819chain 'E' and (resid 29 through 48 )
20E49E8820chain 'E' and (resid 49 through 88 )
21E89E10621chain 'E' and (resid 89 through 106 )
22E107E13122chain 'E' and (resid 107 through 131 )
23E132E21223chain 'E' and (resid 132 through 212 )
24E213E24724chain 'E' and (resid 213 through 247 )
25E248E33525chain 'E' and (resid 248 through 335 )
26F9F12226chain 'F' and (resid 9 through 122 )
27F123F24727chain 'F' and (resid 123 through 247 )
28F248F33528chain 'F' and (resid 248 through 335 )
29G9G2829chain 'G' and (resid 9 through 28 )
30G29G8830chain 'G' and (resid 29 through 88 )
31G89G13131chain 'G' and (resid 89 through 131 )
32G132G14832chain 'G' and (resid 132 through 148 )
33G149G21233chain 'G' and (resid 149 through 212 )
34G213G24734chain 'G' and (resid 213 through 247 )
35G248G29035chain 'G' and (resid 248 through 290 )
36G291G33536chain 'G' and (resid 291 through 335 )
37H9H2837chain 'H' and (resid 9 through 28 )
38H29H8838chain 'H' and (resid 29 through 88 )
39H89H10639chain 'H' and (resid 89 through 106 )
40H107H12240chain 'H' and (resid 107 through 122 )
41H123H15541chain 'H' and (resid 123 through 155 )
42H156H21242chain 'H' and (resid 156 through 212 )
43H213H23143chain 'H' and (resid 213 through 231 )
44H232H27444chain 'H' and (resid 232 through 274 )
45H275H33545chain 'H' and (resid 275 through 335 )

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