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 :  QR15, AN ALDOLASE
 
Authors :  A. Y. Tan, P. C. Smith, J. Shen, R. Xiao, T. Acton, B. Rost, G. Montelione, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  07 Oct 02  (Deposition) - 04 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Barrel, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Aldolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Y. Tan, P. C. Smith, J. Shen, R. Xiao, T. Acton, B. Rost, G. Montelione, J. F. Hunt
Crystal Structure Of Aquifex Aeolicus Aldolase, Northeast Structural Genomics Consortium Target Qr15
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: PHOSPHODEOXYRIBOALDOLASE, DEOXYRIBOALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:1254 , GLY B:1282 , GLY B:1283 , SER B:1304 , HOH B:2126 , HOH B:2161BINDING SITE FOR RESIDUE PO4 B 3001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:162 -Pro A:163
2Phe B:1162 -Pro B:1163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MZH)

(-) Exons   (0, 0)

(no "Exon" information available for 1MZH)

(-) 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:225
 aligned with DEOC_AQUAE | O66540 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:225
                                                                                                                                                                                                                                                    219      
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        |-     
          DEOC_AQUAE      1 MIDVRKYIDNAALKPHLSEKEIEEFVLKSEELGIYAVCVNPYHVKLASSIAKKVKVCCVIGFPLGLNKTSVKVKEAVEAVRDGAQELDIVWNLSAFKSEKYDFVVEELKEIFRETPSAVHKVIVETPYLNEEEIKKAVEICIEAGADFIKTSTGFAPRGTTLEEVRLIKSSAKGRIKVKASGGIRDLETAISMIEAGADRIGTSSGISIAEEFLKRHLI------    -
               SCOP domains d1mzha_ A: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                    SCOP domains
               CATH domains 1mzhA00 A:101-325 Aldolase class I                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeee.....hhhhhhhhhhhhhhh...eeee...hhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mzh A  101 MIDVRKYIDNAALKPHLSEKEIEEFVLKSEELGIYAVCVNPYHVKLASSIAKKVKVCCVIGFPLGLNKTSVKVKEAVEAVRDGAQELDIVWNLSAFKSEKYDFVVEELKEIFRETPSAVHKVIVETPYLNEEEIKKAVEICIEAGADFIKTSTGFAPRGTTLEEVRLIKSSAKGRIKVKASGGIRDLETAISMIEAGADRIGTSSGISIAEEFLKRHLILEHHHH  325
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320     


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with DEOC_AQUAE | O66540 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:221
                                                                                                                                                                                                                                                    219  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        |- 
          DEOC_AQUAE      1 MIDVRKYIDNAALKPHLSEKEIEEFVLKSEELGIYAVCVNPYHVKLASSIAKKVKVCCVIGFPLGLNKTSVKVKEAVEAVRDGAQELDIVWNLSAFKSEKYDFVVEELKEIFRETPSAVHKVIVETPYLNEEEIKKAVEICIEAGADFIKTSTGFAPRGTTLEEVRLIKSSAKGRIKVKASGGIRDLETAISMIEAGADRIGTSSGISIAEEFLKRHLI--    -
               SCOP domains d1mzhb_ B: Deoxyribose-phosphate aldolase DeoC                                                                                                                                                                                SCOP domains
               CATH domains 1mzhB00 B:1101-1321 Aldolase class I                                                                                                                                                                                          CATH domains
           Pfam domains (1) --DeoC-1mzhB01 B:1103-1312                                                                                                                                                                                          --------- Pfam domains (1)
           Pfam domains (2) --DeoC-1mzhB02 B:1103-1312                                                                                                                                                                                          --------- Pfam domains (2)
         Sec.struct. author ..hhhh.eeeee.....hhhhhhhhhhhhhhh...eeee...hhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mzh B 1101 MIDVRKYIDNAALKPHLSEKEIEEFVLKSEELGIYAVCVNPYHVKLASSIAKKVKVCCVIGFPLGLNKTSVKVKEAVEAVRDGAQELDIVWNLSAFKSEKYDFVVEELKEIFRETPSAVHKVIVETPYLNEEEIKKAVEICIEAGADFIKTSTGFAPRGTTLEEVRLIKSSAKGRIKVKASGGIRDLETAISMIEAGADRIGTSSGISIAEEFLKRHLILE 1321
                                  1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)
(-)
Family: DeoC (21)
(-)
Aquifex aeolicus (1)
1aDeoC-1mzhB01B:1103-1312
1bDeoC-1mzhB02B:1103-1312

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEOC_AQUAE | O66540)
molecular function
    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:0004139    deoxyribose-phosphate aldolase activity    Catalysis of the reaction: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.
    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:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0009264    deoxyribonucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0046386    deoxyribose phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of deoxyribose phosphate, the phosphorylated sugar 2-deoxy-erythro-pentose.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:162 - Pro A:163   [ RasMol ]  
    Phe B:1162 - Pro B:1163   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  1mzh
    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
  DEOC_AQUAE | O66540
    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)
  4.1.2.4
    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
  DEOC_AQUAE | O66540
    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 1MZH)

(-) Related Entries Specified in the PDB File

qr15