Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF L-2-KETO-3-DEOXYARABONATE DEHYDRATASE
 
Authors :  N. Shimada, B. Mikami
Date :  17 Dec 08  (Deposition) - 12 Jan 10  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Dhdps/Nal Family, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shimada, B. Mikami, S. Watanabe, T. Kodaki, K. Makino
Structural Analysis Of L -2-Keto-3-Deoxyarabonate Dehydratase An Enzyme Involved In An Alternative Bacterial Pathway Of L-Arabinose Metabolism In Complex With Pyruvate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-2-KETO-3-DEOXYARABONATE DEHYDRATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ARAD
    Organism Scientific: AZOSPIRILLUM BRASILENSE
    Organism Taxid: 192

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:220 , ALA A:306 , ARG A:310 , HOH A:495 , HOH A:755 , HOH A:757BINDING SITE FOR RESIDUE PO4 A 1001
2AC2SOFTWAREHIS B:220 , HIS B:248 , ALA B:306 , ARG B:310 , HOH B:680 , HOH B:876 , HOH B:882BINDING SITE FOR RESIDUE PO4 B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:291 -Pro A:292
2His B:291 -Pro B:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FKK)

(-) 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:304
 aligned with KDADA_AZOBR | Q1JUQ0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:304
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305    
          KDADA_AZOBR     6 TPRHRGIFPVVPTTFADTGELDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFKIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 309
               SCOP domains d3fkka_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..............hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh...ee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkk A  17 TPRHRGIFPVVPTTFADTGDLDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFKIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 320
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316    


Chain B from PDB  Type:PROTEIN  Length:304
 aligned with KDADA_AZOBR | Q1JUQ0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:304
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305    
          KDADA_AZOBR     6 TPRHRGIFPVVPTTFADTGELDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFKIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 309
               SCOP domains d3fkkb_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..............hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkk B  17 TPRHRGIFPVVPTTFADTGDLDLASQKRAVDFMIDAGSDGLCILANFSEQFAITDDERDVLTRTILEHVAGRVPVIVTTSHYSTQVCAARSLRAQQLGAAMVMAMPPYHGATFRVPEAQIFEFYARVSDAIAIPIMVQDAPASGTALSAPFLARMAREIEQVAYFKIETPGAANKLRELIRLGGDAIEGPWDGEEAITLLADLHAGATGAMTGGGFPDGIRPILEAWREGRHDDAYARYQAWLPLINHENRQSGILTAKALMREGGVIASERPRHPMPELHPDTRAELLAIARRLDPLVLRWAH 320
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FKK)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDADA_AZOBR | Q1JUQ0)
molecular function
    GO:0047449    2-dehydro-3-deoxy-L-arabinonate dehydratase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-L-arabinonate = 2,5-dioxopentanoate + H(2)O.
    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: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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019570    L-arabinose catabolic process to 2-oxoglutarate    The chemical reactions and pathways resulting in the breakdown of L-arabinose into other compounds, including 2-oxoglutarate.
    GO:0019568    arabinose catabolic process    The chemical reactions and pathways resulting in the breakdown of arabinose, arabino-pentose.
    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.
    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.

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:291 - Pro A:292   [ RasMol ]  
    His B:291 - Pro B:292   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  3fkk
    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
  KDADA_AZOBR | Q1JUQ0
    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)
  (no 'Enzyme Classificator' available)
    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
  KDADA_AZOBR | Q1JUQ0
    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
        KDADA_AZOBR | Q1JUQ0: 3fkr

(-) Related Entries Specified in the PDB File

3fkr