Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE APOENZYME FROM TRYPANOSOMA BRUCEI.
 
Authors :  J. Martinez-Oyanedel, I. W. Mcnae, L. A. Fothergill-Gilmore, M. D. Wal
Date :  29 Jun 06  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Martinez-Oyanedel, I. W. Mcnae, M. W. Nowicki, J. W. Keillor, P. A. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw
The First Crystal Structure Of Phosphofructokinase From A Eukaryote: Trypanosoma Brucei.
J. Mol. Biol. V. 366 1185 2007
PubMed-ID: 17207816  |  Reference-DOI: 10.1016/J.JMB.2006.10.019

(-) Compounds

Molecule 1 - 6-PHOSPHO-1-FRUCTOKINASE
    Chains: A, B
    EC Number: 2.7.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PFK
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Synonym: ATP-DEPENDENT PHOSPHOFRUCTOKINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:259 , VAL A:260 , ALA A:262 , ARG A:317 , SER A:318BINDING SITE FOR RESIDUE NA A 488
2AC2SOFTWAREALA B:259 , VAL B:260 , ALA B:262 , ARG B:317 , SER B:318 , HOH B:532BINDING SITE FOR RESIDUE NA B 488

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HIG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HIG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HIG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HIG)

(-) Exons   (0, 0)

(no "Exon" information available for 2HIG)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:440
 aligned with PFKA_TRYBB | O15648 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:447
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       
           PFKA_TRYBB     9 VTSKLVKAHRAMLNSVTQEDLKVDRLPGADYPNPSKKYSSRTEFRDKTDYIMYNPRPRDEPSSENPVSVSPLLCELAAARSRIHFNPTETTIGIVTCGGICPGLNDVIRSITLTGINVYNVKRVIGFRFGYWGLSKKGSQTAIELHRGRVTNIHHYGGTILGSSRGPQDPKEMVDTLERLGVNILFTVGGDGTQRGALVISQEAKRRGVDISVFGVPKTIDNDLSFSHRTFGFQTAVEKAVQAIRAAYAEAVSANYGVGVVKLMGRDSGFIAAQAAVASAQANICLVPENPISEQEVMSLLERRFCHSRSCVIIVAEGFGQDWGRGSGGYDASGNKKLIDIGVILTEKVKAFLKANKSRYPDSTVKYIDPSYMIRACPPSANDALFCATLATLAVHEAMAGATGCIIAMRHNNYILVPIKVATSVRRVLDLRGQLWRQVREITVDLG 455
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee................ee.....ee....hhhhhhhh.....eee.......-----........eeee.....ee..hhhh.eeeeee......hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh..eeehhhhhhhhhhh............hhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh...eee......hhhhhhhhhhhhh....eeeeeee...hhhhh.--............hhhhhhhhhhhhhhhh........eeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhh.ee.eeeeee..eeeeeehhhhh.eeeee...hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hig A   9 VTSKLVKAHRAMLNSVTQEDLKVDRLPGADYPNPSKKYSSRTEFRDKTDYIMYNPRPRD-----NPVSVSPLLCELAAARSRIHFNPTETTIGIVTCGGICPGLNDVIRSITLTGINVYNVKRVIGFRFGYWGLSKKGSQTAIELHRGRVTNIHHYGGTILGSSRGPQDPKEMVDTLERLGVNILFTVGGDGTQRGALVISQEAKRRGVDISVFGVPKTIDNDLSFSHRTFGFQTAVEKAVQAIRAAYAEAVSANYGVGVVKLMGRDSGFIAAQAAVASAQANICLVPENPISEQEVMSLLERRFCHSRSCVIIVAEGFGQDWGR--GGYDASGNKKLIDIGVILTEKVKAFLKANKSRYPDSTVKYIDPSYMIRACPPSANDALFCATLATLAVHEAMAGATGCIIAMRHNNYILVPIKVATSVRRVLDLRGQLWRQVREITVDLG 455
                                    18        28        38        48        58        |-    |   78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    |  338       348       358       368       378       388       398       408       418       428       438       448       
                                                                                     67    73                                                                                                                                                                                                                                                                 333  |                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                 336                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:422
 aligned with PFKA_TRYBB | O15648 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:447
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       
           PFKA_TRYBB     9 VTSKLVKAHRAMLNSVTQEDLKVDRLPGADYPNPSKKYSSRTEFRDKTDYIMYNPRPRDEPSSENPVSVSPLLCELAAARSRIHFNPTETTIGIVTCGGICPGLNDVIRSITLTGINVYNVKRVIGFRFGYWGLSKKGSQTAIELHRGRVTNIHHYGGTILGSSRGPQDPKEMVDTLERLGVNILFTVGGDGTQRGALVISQEAKRRGVDISVFGVPKTIDNDLSFSHRTFGFQTAVEKAVQAIRAAYAEAVSANYGVGVVKLMGRDSGFIAAQAAVASAQANICLVPENPISEQEVMSLLERRFCHSRSCVIIVAEGFGQDWGRGSGGYDASGNKKLIDIGVILTEKVKAFLKANKSRYPDSTVKYIDPSYMIRACPPSANDALFCATLATLAVHEAMAGATGCIIAMRHNNYILVPIKVATSVRRVLDLRGQLWRQVREITVDLG 455
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........hhhhhh.ee.....ee...------------..eee......-.............eeee.....ee..hhhh.eeeeee......hhhhhhhhhhhhhhhhh...eeee..hhhhhhh.hhhhh.eeehhhhhhhhhhh............hhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh....eeeeee..............hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh...eee......hhhhhhhhhhhhhhh..eeeeeee.......------------....hhhhhhhhhhhhhhhh........eeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhh.ee.eeeeee..eeeeeehhhhh.eeeee...hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hig B   9 VTSKLVKAHRAMLNSVTQEDLKVDRLPGADYPNPS------------TDYIMYNPRPR-EPSSENPVSVSPLLCELAAARSRIHFNPTETTIGIVTCGGICPGLNDVIRSITLTGINVYNVKRVIGFRFGYWGLSKKGSQTAIELHRGRVTNIHHYGGTILGSSRGPQDPKEMVDTLERLGVNILFTVGGDGTQRGALVISQEAKRRGVDISVFGVPKTIDNDLSFSHRTFGFQTAVEKAVQAIRAAYAEAVSANYGVGVVKLMGRDSGFIAAQAAVASAQANICLVPENPISEQEVMSLLERRFCHSRSCVIIVAEGFGQDW------------KKLIDIGVILTEKVKAFLKANKSRYPDSTVKYIDPSYMIRACPPSANDALFCATLATLAVHEAMAGATGCIIAMRHNNYILVPIKVATSVRRVLDLRGQLWRQVREITVDLG 455
                                    18        28        38    |    -       |58       |68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328  |      -     | 348       358       368       378       388       398       408       418       428       438       448       
                                                             43           56        66 |                                                                                                                                                                                                                                                                    331          344                                                                                                               
                                                                                      68
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2HIG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HIG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HIG)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PFKA_TRYBB | O15648)
molecular function
    GO:0003872    6-phosphofructokinase activity    Catalysis of the reaction: ATP + D-fructose-6-phosphate = ADP + D-fructose 1,6-bisphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006002    fructose 6-phosphate metabolic process    The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0061615    glycolytic process through fructose-6-phosphate    The chemical reactions and pathways resulting in the breakdown of a monosaccharide into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0020015    glycosome    A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hig)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2hig
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PFKA_TRYBB | O15648
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.11
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PFKA_TRYBB | O15648
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PFKA_TRYBB | O15648: 3cvl 3f5m

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2HIG)