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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE (KDPG) ALDOLASE FROM PSEUDOMONAS PUTIDA.
 
Authors :  L. Watanabe, B. J. Bell, L. Lebioda, J. L. Rios-Steiner, A. Tulinsky, R.
Date :  03 Oct 02  (Deposition) - 16 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  2-Keto-3-Deoxy-6-Phosphogluconate Aldolase, Sulfate, Beta-Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Bell, L. Watanabe, J. L. Rios-Steiner, A. Tulinsky, L. Lebioda, R. K. Arni
Structure Of 2-Keto-3-Deoxy-6-Phosphogluconate (Kdpg) Aldolase From Pseudomonas Putida.
Acta Crystallogr. , Sect. D V. 59 1454 2003
PubMed-ID: 12876349  |  Reference-DOI: 10.1107/S0907444903013192
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KDPG ALDOLASE
    Chains: A
    EC Number: 4.1.2.14
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:174 , GLY A:175 , THR A:195 , THR A:196 , HOH A:305BINDING SITE FOR RESIDUE SO4 A 299
2AC2SOFTWAREGLU A:57 , ARG A:61 , GLY A:84 , THR A:85 , VAL A:104 , THR A:105 , PRO A:106 , LYS A:145BINDING SITE FOR RESIDUE SO4 A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MXS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:147 -Pro A:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MXS)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_KDPG_KHG_1PS00159 KDPG and KHG aldolases active site.ALKD_PSEPU52-61  1A:52-61
2ALDOLASE_KDPG_KHG_2PS00160 KDPG and KHG aldolases Schiff-base forming residue.ALKD_PSEPU140-153  1A:140-153
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_KDPG_KHG_1PS00159 KDPG and KHG aldolases active site.ALKD_PSEPU52-61  3A:52-61
2ALDOLASE_KDPG_KHG_2PS00160 KDPG and KHG aldolases Schiff-base forming residue.ALKD_PSEPU140-153  3A:140-153

(-) Exons   (0, 0)

(no "Exon" information available for 1MXS)

(-) 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:216
 aligned with ALKD_PSEPU | P00885 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:216
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           ALKD_PSEPU    11 LSMADKAARIDAICEKARILPVITIAREEDILPLADALAAGGIRTLEVTLRSQHGLKAIQVLREQRPELCVGAGTVLDRSMFAAVEAAGAQFVVTPGITEDILEAGVDSEIPLLPGISTPSEIMMGYALGYRRFKLFPAEISGGVAAIKAFGGPFGDIRFCPTGGVNPANVRNYMALPNVMCVGTGWMLDSSWIKNGDWARIEACSAEAIALLDAN 226
               SCOP domains d1mxsa_ A: KDPG aldolase                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxsA00 A:11-226 Aldolase class I                                                                                                                                                                                        CATH domains
               Pfam domains ---------Aldolase-1mxsA01 A:20-215                                                                                                                                                                           ----------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh...ee....hhhhhhhhhhh...ee.ee.hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.....eeee.......hhhhhhhh.....eee....hhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------ALDOLASE_K------------------------------------------------------------------------------ALDOLASE_KDPG_------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mxs A  11 LSMADKAARIDAICEKARILPVITIAREEDILPLADALAAGGIRTLEVTLRSQHGLKAIQVLREQRPELCVGAGTVLDRSMFAAVEAAGAQFVVTPGITEDILEAGVDSEIPLLPGISTPSEIMMGYALGYRRFKLFPAEISGGVAAIKAFGGPFGDIRFCPTGGVNPANVRNYMALPNVMCVGTTWMLDSSWIKNGDWARIEACSAEAIALLDAN 226
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALKD_PSEPU | P00885)
molecular function
    GO:0008675    2-dehydro-3-deoxy-phosphogluconate aldolase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate.
    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.
biological process
    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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:147 - Pro A:148   [ RasMol ]  
 
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
  1mxs
    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
  ALKD_PSEPU | P00885
    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)
  4.1.2.14
    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
  ALKD_PSEPU | P00885
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1MXS)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MXS)