[English] 日本語
Yorodumi
- PDB-4pfk: PHOSPHOFRUCTOKINASE. STRUCTURE AND CONTROL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pfk
TitlePHOSPHOFRUCTOKINASE. STRUCTURE AND CONTROL
ComponentsPHOSPHOFRUCTOKINASE
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / monosaccharide binding / fructose 6-phosphate metabolic process / canonical glycolysis / AMP binding / ATP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / monosaccharide binding / fructose 6-phosphate metabolic process / canonical glycolysis / AMP binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsEvans, P.R. / Hudson, P.J.
Citation
Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: Phosphofructokinase: structure and control.
Authors: Evans, P.R. / Farrants, G.W. / Hudson, P.J.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Unliganded Phosphofructokinase from Escherichia Coli
Authors: Rypniewski, W.R. / Evans, P.R.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of the Complex of Phosphofructokinase from Escherichia Coli with its Reaction Products
Authors: Shirakihara, Y. / Evans, P.R.
#3: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallographic Structure of Allosterically Inhibited Phosphofructokinase at 7 Angstroms Resolution
Authors: Evans, P.R. / Farrants, G.W. / Lawrence, M.C.
#4: Journal: Eur.J.Biochem. / Year: 1985
Title: Nucleotide Sequence and High-Level Expression of the Major Escherichia Coli Phosphofructokinase
Authors: Hellinga, H.W. / Evans, P.R.
#5: Journal: Nature / Year: 1979
Title: Structure and Control of Phosphofructokinase from Bacillus Stearothermophilus
Authors: Evans, P.R. / Hudson, P.J.
#6: Journal: Proc.FEBS Meet. / Year: 1978
Title: The Three-Dimensional Structure of Phosphofructokinase from Bacillus Stearothermophilus
Authors: Evans, P.R. / Hudson, P.J.
History
DepositionJan 25, 1988Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOFRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3306
Polymers34,1671
Non-polymers1,1635
Water1,26170
1
A: PHOSPHOFRUCTOKINASE
hetero molecules

A: PHOSPHOFRUCTOKINASE
hetero molecules

A: PHOSPHOFRUCTOKINASE
hetero molecules

A: PHOSPHOFRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,32024
Polymers136,6674
Non-polymers4,65320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area23530 Å2
ΔGint-193 kcal/mol
Surface area38730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.500, 84.100, 61.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

21A-380-

HOH

-
Components

#1: Protein PHOSPHOFRUCTOKINASE


Mass: 34166.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: 293 / Strain (production host): 293 / References: UniProt: P00512, 6-phosphofructokinase
#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.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growDetails: THE CRYSTALS USED IN THIS STUDY WERE GROWN FROM POTASSIUM PHOSPHATE WITH 2 MILLIMOLAR FRUCTOSE-6-PHOSPHATE. FOR THIS LIGANDED STRUCTURE, THE CRYSTALS WERE SOAKED IN FRUCTOSE-6-PHOSPHATE (F6P) ...Details: THE CRYSTALS USED IN THIS STUDY WERE GROWN FROM POTASSIUM PHOSPHATE WITH 2 MILLIMOLAR FRUCTOSE-6-PHOSPHATE. FOR THIS LIGANDED STRUCTURE, THE CRYSTALS WERE SOAKED IN FRUCTOSE-6-PHOSPHATE (F6P) AND ADP/MG IN POTASSIUM TARTRATE. F6P 323 AND THE EFFECTOR SITE ADP 326 ARE TREATED AS FULLY OCCUPIED WHILE ADP 324 IS TREATED AS HALF OCCUPIED.
Crystal grow
*PLUS
pH: 7.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mpotassium phosphate11
22 mMF6P11

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→30 Å / Rfactor obs: 0.169
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 72 70 2534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.041

+
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