[English] 日本語
Yorodumi
- PDB-1kz8: CRYSTAL STRUCTURE OF PORCINE FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kz8
TitleCRYSTAL STRUCTURE OF PORCINE FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH A NOVEL ALLOSTERIC-SITE INHIBITOR
ComponentsFRUCTOSE-1,6-BISPHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Gluconeogenesis / 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 / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process ...Gluconeogenesis / 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 / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process / regulation of gluconeogenesis / dephosphorylation / AMP binding / gluconeogenesis / negative regulation of cell growth / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / metal ion binding / identical protein binding / nucleus / 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
ADENOSINE MONOPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / : / Chem-PFE / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsWright, S.W. / Carlo, A.A. / Carty, M.D. / Danley, D.E. / Hageman, D.L. / Karam, G.A. / Levy, C.B. / Mansour, M.N. / Mathiowetz, A.M. / McClure, L.D. ...Wright, S.W. / Carlo, A.A. / Carty, M.D. / Danley, D.E. / Hageman, D.L. / Karam, G.A. / Levy, C.B. / Mansour, M.N. / Mathiowetz, A.M. / McClure, L.D. / Nestor, N.B. / McPherson, R.K. / Pandit, J. / Pustilnik, L.R. / Schulte, G.K. / Soeller, W.C. / Treadway, J.L. / Wang, I.-K. / Bauer, P.H.
CitationJournal: J.MED.CHEM. / Year: 2002
Title: ANILINOQUINAZOLINE INHIBITORS OF FRUCTOSE 1,6-BISPHOSPHATASE BIND AT A NOVEL ALLOSTERIC SITE: SYNTHESIS, IN VITRO CHARACTERIZATION, AND X-RAY CRYSTALLOGRAPHY
Authors: Wright, S.W. / Carlo, A.A. / Carty, M.D. / Danley, D.E. / Hageman, D.L. / Karam, G.A. / Levy, C.B. / Mansour, M.N. / Mathiowetz, A.M. / McClure, L.D. / Nestor, N.B. / McPherson, R.K. / ...Authors: Wright, S.W. / Carlo, A.A. / Carty, M.D. / Danley, D.E. / Hageman, D.L. / Karam, G.A. / Levy, C.B. / Mansour, M.N. / Mathiowetz, A.M. / McClure, L.D. / Nestor, N.B. / McPherson, R.K. / Pandit, J. / Pustilnik, L.R. / Schulte, G.K. / Soeller, W.C. / Treadway, J.L. / Wang, I.-K. / Bauer, P.H.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE Residues 20, 96 and 199 are in conflict in swissprot entry P00636. Residue 20 can be GLU ... SEQUENCE Residues 20, 96 and 199 are in conflict in swissprot entry P00636. Residue 20 can be GLU or GLN, 96 can be SER or THR and residue 199 can be ASP or ASN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FRUCTOSE-1,6-BISPHOSPHATASE
F: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,57610
Polymers73,4072
Non-polymers2,1708
Water9,728540
1
A: FRUCTOSE-1,6-BISPHOSPHATASE
F: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules

A: FRUCTOSE-1,6-BISPHOSPHATASE
F: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,15220
Polymers146,8134
Non-polymers4,33916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area24290 Å2
ΔGint-145 kcal/mol
Surface area41370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.650, 165.940, 79.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Sugars , 2 types, 4 molecules AF

#1: Protein FRUCTOSE-1,6-BISPHOSPHATASE / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase / FBPase


Mass: 36703.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: P00636, fructose-bisphosphatase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 546 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-PFE / {4-[3-(6,7-DIETHOXY-QUINAZOLIN-4-YLAMINO)-PHENYL]-THIAZOL-2-YL}-METHANOL


Mass: 422.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N4O3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mMpotassium phosphate1droppH7.2
21 mMEDTA1drop
31 mMbeta-mercaptoethanol1drop
40.5 mM1dropMgCl2
51 mM251drop
615 mg/mlprotein1drop
7100 mMHEPES1reservoirpH7.0
8200 mMsodium acetate1reservoir
913.5 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 24, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 54052 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 29.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 7.77 / % possible all: 93.9
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Rmerge(I) obs: 0.214

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMAC5refinement
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ID 1FPD

1fpd


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.832 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21445 2681 5.1 %RANDOM
Rwork0.1773 ---
obs0.17918 49955 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.821 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2---0.59 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 140 540 5562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225114
X-RAY DIFFRACTIONr_bond_other_d0.0020.024736
X-RAY DIFFRACTIONr_angle_refined_deg2.1362.0126930
X-RAY DIFFRACTIONr_angle_other_deg1.197311046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9643634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.71515953
X-RAY DIFFRACTIONr_chiral_restr0.1210.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025522
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02954
X-RAY DIFFRACTIONr_nbd_refined0.2280.31200
X-RAY DIFFRACTIONr_nbd_other0.2210.34738
X-RAY DIFFRACTIONr_nbtor_other0.0830.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.5606
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3450.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.328
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.359
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.533
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.671.53166
X-RAY DIFFRACTIONr_mcangle_it3.01625110
X-RAY DIFFRACTIONr_scbond_it3.53531948
X-RAY DIFFRACTIONr_scangle_it5.54.51820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.25 -
Rwork0.207 3312
all-191
Refinement
*PLUS
Rfactor obs: 0.17918 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / Rfactor Rwork: 0.207

+
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