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

(-) Description

Title :  STRUCTURE OF GIARDIA FRUCTOSE-1,6-BIPHOSPHATE ALDOLASE IN COMPLEX WITH 3-HYDROXY-2-PYRIDONE
 
Authors :  O. Herzberg, A. Galkin
Date :  17 Aug 10  (Deposition) - 19 Jan 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Class Ii Fructose-1, 6-Bisphosphate Aldolase, Glycolytic Pathway, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Li, Z. Liu, D. W. Cho, J. Zou, M. Gong, R. M. Breece, A. Galkin, L. Li, H. Zhao, G. D. Maestas, D. L. Tierney, O. Herzberg, D. Dunaway-Mariano P. S. Mariano
Rational Design, Synthesis And Evaluation Of First Generation Inhibitors Of The Giardia Lamblia Fructose-1, 6-Biphosphate Aldolase.
J. Inorg. Biochem. V. 105 509 2010
PubMed-ID: 21333622  |  Reference-DOI: 10.1016/J.JINORGBIO.2010.12.012

(-) Compounds

Molecule 1 - PUTATIVE FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
    ChainsA, B
    EC Number4.1.2.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)STAR
    Expression System Taxid562
    Expression System Vector TypePET100/D-TOPO
    GeneALD, FBPA
    Organism CommonGIARDIA INTESTINALIS
    Organism ScientificGIARDIA INTESTINALIS
    Organism Taxid5741
    StrainWB

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1HDX2Ligand/Ion({3-HYDROXY-2-OXO-4-[2-(PHOSPHONOOXY)ETHYL]PYRIDIN-1(2H)-YL}METHYL)PHOSPHONIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:84 , HIS A:178 , HIS A:210 , HDX A:341BINDING SITE FOR RESIDUE ZN A 340
2AC2SOFTWAREASN A:24 , SER A:50 , ASP A:83 , HIS A:84 , HIS A:178 , GLY A:179 , LYS A:182 , GLY A:211 , SER A:212 , SER A:213 , ASN A:253 , ASP A:255 , SER A:256 , ARG A:259 , ZN A:340 , HOH A:389 , ARG B:280BINDING SITE FOR RESIDUE HDX A 341
3AC3SOFTWAREHIS B:84 , HIS B:178 , HIS B:210 , HDX B:343BINDING SITE FOR RESIDUE ZN B 342
4AC4SOFTWAREARG A:280 , ASN B:24 , GLN B:48 , SER B:50 , ASP B:83 , HIS B:84 , HIS B:178 , GLY B:179 , LYS B:182 , GLY B:211 , SER B:212 , SER B:213 , ASN B:253 , ASP B:255 , SER B:256 , ARG B:259 , ZN B:342 , HOH B:420BINDING SITE FOR RESIDUE HDX B 343

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OHI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OHI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OHI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OHI)

(-) Exons   (0, 0)

(no "Exon" information available for 3OHI)

(-) Sequences/Alignments

Asymmetric/Biological 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:319
 aligned with O97447_GIAIN | O97447 from UniProtKB/TrEMBL  Length:323

    Alignment length:322
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
         O97447_GIAIN     2 PLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKEVVAYAHARSVSVEAELGTLGGIEEDVQNTVQLTEPQDAKKFVELTGVDALAVAIGTSHGAYKFKSESDIRLAIDRVKTISDLTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKIKAFGSAGHAGDYKVVSLEEAKAWYK 323
               SCOP domains d3ohia_ A: automated matches                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhh.hhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeee.......---.......hhhhhhhhhhhhh..eeee...................hhhhhhhhhhhhh..eee......hhhhhhhhhhh..........hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ohi A   2 PLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKEVVAYAHARSVSVEAELGTLGGIE---QNTVQLTEPQDAKKFVELTGVDALAVAIGTSHGAYKFKSESDIRLAIDRVKTISDLTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKIKAFGSAGHAGDYKVVSLEEAKAWYK 323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 |   | 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
                                                                                                                                                                       143 147                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:318
 aligned with O97447_GIAIN | O97447 from UniProtKB/TrEMBL  Length:323

    Alignment length:322
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
         O97447_GIAIN     2 PLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKEVVAYAHARSVSVEAELGTLGGIEEDVQNTVQLTEPQDAKKFVELTGVDALAVAIGTSHGAYKFKSESDIRLAIDRVKTISDLTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKIKAFGSAGHAGDYKVVSLEEAKAWYK 323
               SCOP domains d3ohib_ B: automated matches                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) F_bP_aldolase-3ohiB01 B:2-307                                                                                                                                                                                                                                                                                     ---------------- Pfam domains (1)
           Pfam domains (2) F_bP_aldolase-3ohiB02 B:2-307                                                                                                                                                                                                                                                                                     ---------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeeeeehhhhhhh.hhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh..eeeee........----......hhhhhhhhhhhhh..eee.....................hhhhhhhhhhhh..eee......hhhhhhhhhhh..........hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ohi B   2 PLCTLRQMLGEARKHKYGVGAFNVNNMEQIQGIMKAVVQLKSPVILQCSRGALKYSDMIYLKKLCEAALEKHPDIPICIHLDHGDTLESVKMAIDLGFSSVMIDASHHPFDENVRITKEVVAYAHARSVSVEAELGTLGGIE----NTVQLTEPQDAKKFVELTGVDALAVAIGTSHGAYKFKSESDIRLAIDRVKTISDLTGIPLVMHGSSSVPKDVKDMINKYGGKMPDAVGVPIESIVHAIGEGVCKINVDSDSRMAMTGAIRKVFVEHPEKFDPRDYLGPGRDAITEMLIPKIKAFGSAGHAGDYKVVSLEEAKAWYK 323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 |    |151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
                                                                                                                                                                       143  148                                                                                                                                                                               

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OHI)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O97447_GIAIN | O97447)
molecular function
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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:0004332    fructose-bisphosphate aldolase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    HDX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ohi)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ohi
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O97447_GIAIN | O97447
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.1.2.13
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  O97447_GIAIN | O97447
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O97447_GIAIN | O974472isv 2isw 3gak 3gay 3gb6

(-) Related Entries Specified in the PDB File

2isv STRUCTURE OF GIARDIA FRUCTOSE-1,6-BIPHOSPHATE ALDOLASE IN COMPLEX WITH PHOSPHOGLYCOLOHYDROXAMATE
2isw STRUCTURE OF GIARDIA FRUCTOSE-1,6-BIPHOSPHATE ALDOLASE IN COMPLEX WITH PHOSPHOGLYCOLOHYDROXAMATE
3gak STRUCTURE OF GIARDIA FRUCTOSE-1,6-BIPHOSPHATE ALDOLASE
3gay STRUCTURE OF GIARDIA FRUCTOSE-1,6-BIPHOSPHATE ALDOLASE IN COMPLEX WITH 1,6-DI-O-PHOSPHONO-D-TAGATOSE
3gb6 STRUCTURE OF GIARDIA FRUCTOSE-1,6-BIPHOSPHATE ALDOLASE IN COMPLEX WITH 1,6-DI-O-PHOSPHONO-D-FRUCTOSE