[English] 日本語
Yorodumi
- PDB-2fie: Structure of human liver FBPase complexed with potent benzoxazole... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fie
TitleStructure of human liver FBPase complexed with potent benzoxazole allosteric inhibitors
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / allosteric inhibitors human liver FBPase / benzoxazole / intersubunit allosteric inhibitors of human liver FBPase
Function / homology
Function and homology information


cellular response to raffinose / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / fructose 1,6-bisphosphate metabolic process / negative regulation of Ras protein signal transduction / Gluconeogenesis / monosaccharide binding ...cellular response to raffinose / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / fructose 1,6-bisphosphate metabolic process / negative regulation of Ras protein signal transduction / Gluconeogenesis / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / dephosphorylation / AMP binding / cellular response to cAMP / gluconeogenesis / response to nutrient levels / 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 / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-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 active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-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-A74 / : / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsAbad-Zapatero, C.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Benzoxazole benzenesulfonamides as allosteric inhibitors of fructose-1,6-bisphosphatase.
Authors: Lai, C. / Gum, R.J. / Daly, M. / Fry, E.H. / Hutchins, C. / Abad-Zapatero, C. / von Geldern, T.W.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Benzoxazole benzenesulfonamides are novel allosteric inhibitors of fructose-1,6-bisphosphatase with a distinct binding mode.
Authors: von Geldern, T.W. / Lai, C. / Gum, R.J. / Daly, M. / Sun, C. / Fry, E.H. / Abad-Zapatero, C.
History
DepositionDec 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN REGARDING THE LIGAND A74, THE USER SHOULD REFER TO COMPOUND NO. 48 IN THE MAIN REFERENCE ...HETEROGEN REGARDING THE LIGAND A74, THE USER SHOULD REFER TO COMPOUND NO. 48 IN THE MAIN REFERENCE FOR THIS ENTRY, TABLE 3.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
L: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3598
Polymers147,4384
Non-polymers1,9214
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19640 Å2
ΔGint-119 kcal/mol
Surface area43440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.369, 83.327, 277.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological active unit is the tetramer. Crystal contains four chains in the asymmetric unit (A,D,H,L) and four molecules of the inhibitors here labeled as residue 974. The same thing is true for the related entry 2fhy.

-
Components

#1: Protein
Fructose-1,6-bisphosphatase 1


Mass: 36859.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: 6His-Xpress-huFBP1-pET100-D-TOPO / Production host: Escherichia coli (E. coli)
References: GenBank: 15277851, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: Chemical
ChemComp-A74 / 2,5-DICHLORO-N-[5-METHOXY-7-(6-METHOXYPYRIDIN-3-YL)-1,3-BENZOXAZOL-2-YL]BENZENESULFONAMIDE


Mass: 480.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H15Cl2N3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 290 K / pH: 8
Details: Crystals grown under oil (3:1 parafin:silicon oil). 2 uL+2uL drops. Well solution: 14-18% PEG1000, 0.1 M Tris pH 8.0 Cryo: quick immersion in: 16% PEG1000, 20% PEG400,0.1 M Tris pH 8.0, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2004
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 38431 / Num. obs: 36725 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.16 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3039 / Rsym value: 0.453 / % possible all: 78.6

-
Processing

Software
NameVersionClassification
CNX2002refinement
XDSdata reduction
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: entry 2fhy

2fhy


Resolution: 2.81→19.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 287219.85 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Entries 2fhy, 2fie and 2fix characterize the binding mode of benzoxazoles as allosteric inhibitors of human liver FBPase as described in the associated references. These three entries focus ...Details: Entries 2fhy, 2fie and 2fix characterize the binding mode of benzoxazoles as allosteric inhibitors of human liver FBPase as described in the associated references. These three entries focus on the binding mode and interactions in the proximity of the ligands. The medium to low resolution of the crystallographic data (3.3, 2.95 and 2.8 A) and the limited quality and extent of the available data, especially for entry 2fix, should be considered when trying to extract accurate interatomic distances between the ligands and the protein, at certain regions of the protein exposed to solvent.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3279 10 %RANDOM
Rwork0.197 ---
all0.222 ---
obs0.23 32661 83.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2786 Å2 / ksol: 0.354974 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20 Å2
2---3.94 Å20 Å2
3---6.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-8 Å
Luzzati sigma a0.45 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.81→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9728 0 124 120 9972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 205 9.4 %
Rwork0.335 1979 -
obs-1979 56.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ACCELRYS_CNX_TOPPAR:protein_rep.paramprotein.top
X-RAY DIFFRACTION2ACCELRYS_CNX_TOPPAR:water_rep.paramion.top
X-RAY DIFFRACTION3ACCELRYS_CNX_TOPPAR:ion.param974.top
X-RAY DIFFRACTION4974.par

+
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