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- PDB-5q0c: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

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Basic information

Entry
Database: PDB / ID: 5q0c
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-(4-methoxyphenyl)thiophen-2-yl]sulfonylurea and with fructose-2,6-diphosphate
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / D3R docking / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyGluconeogenesis / Fructose-1-6-bisphosphatase active site. / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1,6-bisphosphatase class 1 / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate metabolic process ...Gluconeogenesis / Fructose-1-6-bisphosphatase active site. / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1,6-bisphosphatase class 1 / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / fructose 1,6-bisphosphate 1-phosphatase activity / fructose metabolic process / gluconeogenesis / Z disc / cell junction / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / metal ion binding / cytosol / cytoplasm / Fructose-1,6-bisphosphatase isozyme 2
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2.4 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-(4-methoxyphenyl)thiophen-2-yl]sulfonylurea and with f2,6p
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 18, 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 isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2
C: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2
E: Fructose-1,6-bisphosphatase isozyme 2
F: Fructose-1,6-bisphosphatase isozyme 2
G: Fructose-1,6-bisphosphatase isozyme 2
H: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,90124
Polyers294,3858
Non-polymers6,51616
Water9,818545
1
A: Fructose-1,6-bisphosphatase isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2
C: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,45012
Polyers147,1924
Non-polymers3,2588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)19130
ΔGint (kcal/M)-89
Surface area (Å2)43720
MethodPISA
2
E: Fructose-1,6-bisphosphatase isozyme 2
F: Fructose-1,6-bisphosphatase isozyme 2
G: Fructose-1,6-bisphosphatase isozyme 2
H: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,45012
Polyers147,1924
Non-polymers3,2588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)19080
ΔGint (kcal/M)-90
Surface area (Å2)43730
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)222.475, 240.518, 138.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: Protein/peptide
Fructose-1,6-bisphosphatase isozyme 2 / FBPase 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase 2 / Muscle FBPase


Mass: 36798.094 Da / Num. of mol.: 8 / Source: (gene. exp.) Homo sapiens (human) / Gene: FBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00757, fructose-bisphosphatase
#2: Chemical
ChemComp-96G / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-5-(4-methoxyphenyl)thiophene-2-sulfonamide


Mass: 474.372 Da / Num. of mol.: 8 / Formula: C15H12BrN3O4S3
#3: Chemical
ChemComp-FDP / FRUCTOSE-2,6-DIPHOSPHATE


Mass: 340.116 Da / Num. of mol.: 8 / Formula: C6H14O12P2 / Fructose 2,6-bisphosphate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 3.26 / Density percent sol: 62.3 %
Crystal growMethod: vapor diffusion, sitting drop
Details: entry deposited much later from experimental date, thus exact crystallization details not known

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Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X10SA / Synchrotron site: SLS / Beamline: X10SA / Wavelength: 0.987
DetectorType: MAR CCD 165 mm / Detector: CCD / Collection date: Jun 12, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 / Relative weight: 1
ReflectionD resolution high: 2.4 / D resolution low: 29.793 / Number obs: 141184 / Percent possible obs: 97.51

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Phasing

PhasingMethod: molecular replacement

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Processing

Software

Language: C++ / Type: package

NameVersionClassificationContact authorContact author emailLocationDate
PHENIX1.11.1_2575refinementPaul D. AdamsPDAdams[at]lbl.govhttp://www.phenix-online.org/
PDB_EXTRACT3.23data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/Dec. 13, 2016
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.28 / Cross valid method: THROUGHOUT / Sigma F: 1.34 / Overall phase error: 23.83 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11 / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 185.73 / B iso mean: 57.1469 / B iso min: 17.1
Least-squares processR factor R free: 0.2103 / R factor R work: 0.1682 / R factor obs: 0.1703 / Highest resolution: 2.4 / Lowest resolution: 29.793 / Number reflection R free: 6943 / Number reflection R work: 134241 / Number reflection obs: 141184 / Percent reflection R free: 4.92 / Percent reflection obs: 97.51
Refine hist #finalHighest resolution: 2.4 / Lowest resolution: 29.793 / B iso mean ligand: 66.91 / B iso mean solvent: 48.99 / Number residues total: 2618
Number of atoms included #finalProtein: 19932 / Nucleic acid: 0 / Ligand: 368 / Solvent: 545 / Total: 20845
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820627
X-RAY DIFFRACTIONf_angle_d0.96027954
X-RAY DIFFRACTIONf_chiral_restr0.0573225
X-RAY DIFFRACTIONf_plane_restr0.0063519
X-RAY DIFFRACTIONf_dihedral_angle_d11.22312388
Refine LS restraints ncs

Ens ID: 1 / Number: 12348 / Refine ID: X-RAY DIFFRACTION / Rms: 5.692 / 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
2.40000.30070.25282.42731863598378479.0000
2.42730.31470.23802.45582013776397783.0000
2.45580.27710.23262.48572013918411986.0000
2.48570.30140.22752.51722284136436491.0000
2.51720.30690.22902.55032064326453295.0000
2.55030.27400.21662.58522044558476299.0000
2.58520.26140.20582.62212474535478299.0000
2.62210.27200.21182.66122434471471499.0000
2.66120.25870.20842.70282494522477199.0000
2.70280.26960.20332.747121245624774100.0000
2.74710.29120.19612.794424045434783100.0000
2.79440.23210.19282.845225945184777100.0000
2.84520.26760.20222.899925345514804100.0000
2.89990.27090.21282.959023045724802100.0000
2.95900.26010.21883.023323245884820100.0000
3.02330.25930.20683.093622745644791100.0000
3.09360.30110.20873.170821945854804100.0000
3.17080.23500.20433.256523245614793100.0000
3.25650.25950.20523.352222045764796100.0000
3.35220.23810.20433.460223445724806100.0000
3.46020.23750.18773.583722346224845100.0000
3.58370.21310.16413.726923045694799100.0000
3.72690.19780.15463.896224746004847100.0000
3.89620.18110.14384.101125145794830100.0000
4.10110.17120.12934.357323346044837100.0000
4.35730.14730.11604.692622446414865100.0000
4.69260.14940.11605.162623746334870100.0000
5.16260.16060.13035.904625546294884100.0000
5.90460.19370.15497.420124847014949100.0000
7.42010.16430.144329.79492724631490396.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.17630.0571-0.14840.0290-0.05750.08070.1527-0.20640.06960.0768-0.1680-0.01810.02940.0412-0.00000.3562-0.01760.01140.3753-0.09590.375553.94685.5753-23.6298
20.0153-0.0003-0.01860.0223-0.03580.05960.0483-0.3837-0.0872-0.1044-0.0363-0.23330.09920.0217-0.00000.3736-0.0282-0.04380.5065-0.06620.315147.47902.3112-10.4508
30.5645-0.2037-0.22500.1693-0.01240.42850.0643-0.11690.0964-0.03380.00350.0478-0.0677-0.03310.00180.23190.00620.01190.2675-0.07700.194731.36049.8582-23.7315
40.1994-0.03060.13270.01930.01810.02340.10550.1454-0.0073-0.1336-0.0576-0.0774-0.07320.05990.00000.32030.00950.00430.3364-0.10410.337853.5315-7.7661-45.7173
5-0.00180.00530.02000.00880.02130.0407-0.07150.2336-0.0291-0.1609-0.0097-0.2075-0.12010.10940.00000.41600.03800.00480.4177-0.10010.294847.3425-4.1490-58.9784
60.1903-0.00470.04920.22630.12220.36850.04280.1131-0.0993-0.0293-0.04060.10590.0350-0.1037-0.00000.3342-0.0087-0.05630.3569-0.09260.340830.6861-10.5385-45.7219
70.20920.1416-0.10480.0806-0.04740.03760.0745-0.03100.1622-0.0160-0.03620.0566-0.01120.0954-0.00000.3285-0.0051-0.01030.3710-0.12630.386965.218410.2867-29.5140
80.0044-0.00490.02850.0438-0.02680.04660.08040.17030.5533-0.0937-0.0881-0.0968-0.1538-0.10230.00010.41110.02120.02300.4396-0.03060.625072.113722.7072-34.5162
90.38370.0417-0.03250.1789-0.07220.33550.1006-0.04380.12800.0820-0.1188-0.1183-0.0103-0.0025-0.00000.3116-0.0263-0.05240.3031-0.03050.375387.92759.7744-25.8999
100.05090.0093-0.00320.0226-0.00110.00370.09520.1315-0.22010.0038-0.08550.00990.09470.0766-0.00000.33320.0217-0.03400.4065-0.11010.345664.2748-16.6111-49.0986
110.05380.0110-0.01440.0676-0.08390.0888-0.0001-0.0262-0.24350.1287-0.16200.08740.0922-0.14180.00010.3734-0.03200.00350.3120-0.02050.404568.1892-21.5489-31.3993
120.21290.07540.09570.35430.27450.3384-0.00080.0532-0.12950.0762-0.0136-0.13510.07310.03440.00000.29030.0497-0.01640.3052-0.04180.366787.0389-14.5522-43.2537
130.1633-0.0936-0.15200.4937-0.02050.1132-0.1222-0.18060.24540.02690.10460.8178-0.3018-0.0565-0.05730.3434-0.0414-0.23790.36740.14470.718394.667853.5036-1.9141
140.5262-0.0059-0.43290.55890.30600.6128-0.4902-0.0751-0.0569-0.14910.30930.72870.33050.2053-0.21930.3469-0.2601-0.33240.22940.05960.414099.745833.9017-8.4156
150.0484-0.09570.02130.23090.03050.0301-0.10910.03550.1687-0.12080.0562-0.2369-0.0625-0.04520.00000.4631-0.0255-0.12140.38000.00990.3997124.762856.87412.9868
160.0308-0.0298-0.01930.01480.01690.0377-0.10190.08300.0380-0.28630.0655-0.4062-0.27820.09830.00000.4712-0.04320.00660.44130.05560.4987136.829250.9761-3.6256
170.2742-0.0941-0.00730.3725-0.00430.1462-0.09120.0124-0.0314-0.02370.0304-0.12040.0768-0.00150.00000.38630.0178-0.04880.32560.03560.3305125.981634.18825.9424
180.1180-0.0047-0.06610.37710.25680.2959-0.1017-0.0052-0.0471-0.58050.18350.09450.13720.11160.16970.5117-0.0619-0.28100.36090.10100.4685104.703467.8393-11.0772
190.1086-0.06890.07100.0375-0.04790.04100.05470.1727-0.2540-0.7995-0.02350.30280.0288-0.18010.07781.0568-0.0505-0.60680.46600.09390.1953106.858174.3508-24.3700
200.2012-0.22630.09260.4930-0.29320.41780.0099-0.1090-0.0080-0.27950.13400.4650-0.0292-0.05790.45200.40080.0019-0.22470.37740.11940.4199100.862490.5397-10.3169
210.0334-0.01030.03940.23380.02130.0287-0.0442-0.0809-0.05540.10110.14870.07430.16820.04760.00010.33530.0104-0.11150.34710.02870.3828120.031567.78659.6452
220.0082-0.0078-0.00680.02790.02280.0334-0.0642-0.1781-0.16610.36260.02260.02460.07640.0370-0.00000.51290.0187-0.09940.48210.04970.3267117.794273.644123.2512
230.1735-0.08100.13120.41140.07180.4121-0.0505-0.02280.04660.10020.0898-0.0975-0.04970.0192-0.00000.3268-0.0041-0.08040.3715-0.00810.3061123.056690.54639.8381
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A9A691chain 'A' and (resid 9 through 69 )
2A70A1192chain 'A' and (resid 70 through 119 )
3A120A3363chain 'A' and (resid 120 through 336 )
4B9B694chain 'B' and (resid 9 through 69 )
5B70B1195chain 'B' and (resid 70 through 119 )
6B120B3366chain 'B' and (resid 120 through 336 )
7C9C697chain 'C' and (resid 9 through 69 )
8C70C1198chain 'C' and (resid 70 through 119 )
9C120C3369chain 'C' and (resid 120 through 336 )
10D9D4910chain 'D' and (resid 9 through 49 )
11D50D11911chain 'D' and (resid 50 through 119 )
12D120D33612chain 'D' and (resid 120 through 336 )
13E9E11913chain 'E' and (resid 9 through 119 )
14E120E33614chain 'E' and (resid 120 through 336 )
15F9F6915chain 'F' and (resid 9 through 69 )
16F70F11916chain 'F' and (resid 70 through 119 )
17F120F33617chain 'F' and (resid 120 through 336 )
18G9G6918chain 'G' and (resid 9 through 69 )
19G70G11919chain 'G' and (resid 70 through 119 )
20G120G33620chain 'G' and (resid 120 through 336 )
21H9H6921chain 'H' and (resid 9 through 69 )
22H70H11922chain 'H' and (resid 70 through 119 )
23H120H33623chain 'H' and (resid 120 through 336 )

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