[English] 日本語
Yorodumi
- PDB-5q06: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5q06
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-[4-(2-methyl-1,3-thiazol-4-yl)phenyl]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 / metal ion binding / nucleus / identical protein binding / 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-95V / 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: 2.4 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-(5-bromo-1,3-thiazol-2-yl)-3-[4-(2-methyl-1,3- ...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-[4-(2-methyl-1,3-thiazol-4-yl)phenyl]sulfonylurea
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)149,2758
Polymers147,4384
Non-polymers1,8374
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-77 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.506, 83.695, 278.843
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 37 or resid 39 through 61 or resid 72 through 335))
21(chain B and (resid 9 through 37 or resid 39 through 335))
31(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))
41(chain D and (resid 9 through 37 or resid 39 through 335))

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
11ASPASPLEULEU(chain A and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))AA9 - 3710 - 38
12THRTHRGLYGLY(chain A and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))AA39 - 6140 - 62
13LYSLYSSERSER(chain A and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))AA72 - 33573 - 336
21ASPASPLEULEU(chain B and (resid 9 through 37 or resid 39 through 335))BB9 - 3710 - 38
22THRTHRSERSER(chain B and (resid 9 through 37 or resid 39 through 335))BB39 - 33540 - 336
31ASPASPLEULEU(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))CC9 - 3710 - 38
32THRTHRGLYGLY(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))CC39 - 6140 - 62
33LYSLYSSERSER(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))CC72 - 33573 - 336
41ASPASPLEULEU(chain D and (resid 9 through 37 or resid 39 through 335))DD9 - 3710 - 38
42THRTHRSERSER(chain D and (resid 9 through 37 or resid 39 through 335))DD39 - 33540 - 336

-
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-95V / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-4-(2-methyl-1,3-thiazol-4-yl)benzene-1-sulfonamide


Mass: 459.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11BrN4O3S3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.43 %
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

-
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: Mar 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→19.986 Å / Num. obs: 62733 / % possible obs: 99.98 %

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.23data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.986 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 3164 5.04 %
Rwork0.168 59569 -
obs0.1713 62733 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.62 Å2 / Biso mean: 29.5649 Å2 / Biso min: 5.15 Å2
Refinement stepCycle: final / Resolution: 2.4→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9729 0 100 704 10533
Biso mean--35.84 34.6 -
Num. residues----1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810037
X-RAY DIFFRACTIONf_angle_d0.99813572
X-RAY DIFFRACTIONf_chiral_restr0.061532
X-RAY DIFFRACTIONf_plane_restr0.0071735
X-RAY DIFFRACTIONf_dihedral_angle_d12.8226086
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6069X-RAY DIFFRACTION10.498TORSIONAL
12B6069X-RAY DIFFRACTION10.498TORSIONAL
13C6069X-RAY DIFFRACTION10.498TORSIONAL
14D6069X-RAY DIFFRACTION10.498TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.43580.30961290.217125562685
2.4358-2.47380.30231470.221325362683
2.4738-2.51430.30951380.217225532691
2.5143-2.55750.29971210.216225672688
2.5575-2.6040.28941360.21325592695
2.604-2.65390.28641460.202325342680
2.6539-2.7080.28361450.198525732718
2.708-2.76670.26451180.192425582676
2.7667-2.83090.25671270.18725862713
2.8309-2.90150.26241500.189825422692
2.9015-2.97970.27781400.191825682708
2.9797-3.06710.32141260.193826042730
3.0671-3.16570.26941360.184825662702
3.1657-3.27840.25491460.173525502696
3.2784-3.4090.24591230.163525972720
3.409-3.56330.22351340.150926022736
3.5633-3.750.20691340.149825892723
3.75-3.98320.20161450.140926322777
3.9832-4.2880.18221330.135425852718
4.288-4.71440.17551520.120626002752
4.7144-5.38490.17981300.131526552785
5.3849-6.74080.19881480.171626852833
6.7408-19.98640.19591600.166327722932
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0839-0.00630.00810.02680.03180.0685-0.02080.0555-0.00990.0273-0.01010.0263-0.1052-0.0744-0.03940.0963-0.00560.01790.0457-0.0090.039416.093543.292216.4848
20.04070.0245-0.03440.037-0.02760.0326-0.03240.08240.0907-0.06280.0103-0.0346-0.05760.0313-0.04890.1183-0.02920.0420.12870.00650.070934.42743.53611.1363
30.016-0.01580.010.0088-0.00970.01130.01670.02180.0071-0.03470.01060.02330.00310.11130.00080.1508-0.06920.01510.15710.00010.11237.061345.77822.8682
40.07380.0151-0.04510.033-0.03640.05950.0022-0.0621-0.07740.0556-0.03840.0591-0.02760.035-0.02470.0520.0056-0.01840.0767-0.01640.082336.423919.058537.231
50.0298-0.0204-0.00580.0083-0.00170.01020.02290.0735-0.0468-0.00620.01540.0005-0.00890.08330.04440.054-0.01550.02130.1364-0.0470.081441.563318.391718.9128
60.00040.0047-0.0010.0562-0.02130.00860.02670.0416-0.01740.07950.01820.02630.00020.11830.02060.07880.01630.00560.1877-0.05030.102249.556616.179116.302
70.00660.00050.00050.0011-0.0020.00580.0077-0.00520.0122-0.0141-0.00380.0019-0.0184-0.00330.00060.16270.0883-0.03890.08310.03180.09066.632653.5325.2106
80.0097-0.00120.01770.02720.0180.0136-0.0075-0.00670.01750.0120.03930.0471-0.09710.0270.03240.11830.03950.0609-0.0285-0.03060.079215.14650.507445.4838
90.0121-0.00040.01360.0499-0.00210.00770.00410.00490.0494-0.02060.02310.0773-0.0266-0.07990.00070.08760.01190.01850.1288-0.00260.1118-5.845839.651347.4394
100.01060.01230.00420.0118-0.00480.0603-0.0175-0.02070.0170.07310.0206-0.0466-0.0113-0.08260.00310.080.03250.01370.079-0.01090.0803-4.780148.804553.7233
110.001600.00120.0008-0.00030.0025-0.0301-0.0163-0.0243-0.0029-0.0093-0.01660.0090.018500.18440.01160.00360.12780.03370.270727.6119.285747.1145
120.0265-0.00580.0110.0162-0.00040.0163-0.02050.0104-0.0341-0.0235-0.0079-0.00280.0085-0.0034-0.02710.08280.01030.02730.0607-0.02340.086710.819519.055333.2027
130.00060.0001-0.00140.00060.00020.00030.01620.0391-0.01290.0055-0.0210.02940.0019-0.00650.00140.05730.02710.00820.0726-0.00330.14225.40855.563737.0245
140.0091-0.0007-0.0050.01520.02540.0426-0.0463-0.0002-0.0377-0.0420.0141-0.009-0.081-0.0347-0.04110.07750.05160.0183-0.00810.0120.09087.298811.004945.9668
150.01860.00940.01490.02510.01380.01120.01670.0079-0.02870.002-0.0117-0.0566-0.01150.01250.02490.045-0.01740.00480.08680.0290.086715.040322.555454.1951
160.0030.00310.0020.00360.00070.0021-0.01520.04110.01520.02370.0418-0.00010.0154-0.00280.00010.1237-0.03010.03460.1540.01930.1059-10.835524.79864.7444
170.00780.0033-0.00650.0208-0.00270.0070.016-0.01920.05240.02640.01180.0005-0.02690.01910.01050.1053-0.0280.01330.0581-0.01750.0658-0.024220.469557.8665
180.00650.0046-0.00250.01480.00210.0014-0.02660.0095-0.00930.01460.00350.06390.0078-0-0.00110.1416-0.00710.03060.10220.0360.1164-2.702211.694761.835
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 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 28 )C9 - 28
8X-RAY DIFFRACTION8chain 'C' and (resid 29 through 170 )C29 - 170
9X-RAY DIFFRACTION9chain 'C' and (resid 171 through 247 )C171 - 247
10X-RAY DIFFRACTION10chain 'C' and (resid 248 through 335 )C248 - 335
11X-RAY DIFFRACTION11chain 'D' and (resid 9 through 28 )D9 - 28
12X-RAY DIFFRACTION12chain 'D' and (resid 29 through 88 )D29 - 88
13X-RAY DIFFRACTION13chain 'D' and (resid 89 through 122 )D89 - 122
14X-RAY DIFFRACTION14chain 'D' and (resid 123 through 179 )D123 - 179
15X-RAY DIFFRACTION15chain 'D' and (resid 180 through 212 )D180 - 212
16X-RAY DIFFRACTION16chain 'D' and (resid 213 through 231 )D213 - 231
17X-RAY DIFFRACTION17chain 'D' and (resid 232 through 290 )D232 - 290
18X-RAY DIFFRACTION18chain 'D' and (resid 291 through 335 )D291 - 335

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more