Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theoretical Model
collapse expand < >
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  PLASMODIUM FALCIPARUM ORNITHINE AMINOTRANSFERASE
 
Authors :  A. Dash
Date :  05 Jun 02  (Deposition) - 19 Jun 02  (Release) - 19 Jun 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Transferase, Aminotransferase, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dash
Plasmodium Falciparum Ornithine Aminotransferase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ORNITHINE AMINOTRANSFERASE
    Chains: A
    EC Number: 2.6.1.13
    Fragment: SEQUENCE DATABASE RESIDUES 6-410, NUMBERED 1-405
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Synonym: ORNITHINE--OXO-ACID AMINOTRANSFERASE

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LX9)

(-) Sites  (0, 0)

(no "Site" information available for 1LX9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LX9)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Gly A:163 -Pro A:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LX9)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.OAT_PLAFD230-267  1A:225-262

(-) Exons   (0, 0)

(no "Exon" information available for 1LX9)

(-) Sequences/Alignments

Theoretical Model
   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:405
 aligned with OAT_PLAFD | Q07805 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:405
                                    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       315       325       335       345       355       365       375       385       395       405     
            OAT_PLAFD     6 ELKSSQDYMNNELTYGAHNYDPIPVVLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFSDSLGVCERYLTNLFGYDKVLMMNTGAEASETAYKLCRKWGYEVKKIPENSAKIIVCNNNFSGRTLGCVSASTDKKCKNNFGPFVPNFLKVPYDDLEALEKELQDPNVCAFIVEPVQGEAGVIVPSDSYFPGVASLCKKYNVLFVADEVQTGLGRTGKLLCTHHYGVKPDVILLGKALSGGHYPISAILANDDVMLVLKPGEHGSTYGGNPLAAAICVEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCAIEFKNDLVNVWDICLKFKENGLITRSVHDKTVRLTPPLCITKEQLDECTEIIVKTVKFF 410
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh........eeeee.......hhhhhhhh.hhhhhh........eeee...hhhhhhhhh....eeeeee..............hhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhh......eeeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeee.....hhhhhhhhhhhh.ee.......eeee......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:225-262   ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lx9 A   1 ELKSSQDYMNNELTYGAHNYDPIPVVLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFSDSLGVCERYLTNLFGYDKVLMMNTGAEASETAYKLCRKWGYEVKKIPENSAKIIVCNNNFSGRTLGCVSASTDKKCKNNFGPFVPNFLKVPYDDLEALEKELQDPNVCAFIVEPVQGEAGVIVPSDSYFPGVASLCKKYNVLFVADEVQTGLGRTGKLLCTHHYGVKPDVILLGKALSGGHYPISAILANDDVMLVLKPGEHGSTYGGNPLAAAICVEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCAIEFKNDLVNVWDICLKFKENGLITRSVHDKTVRLTPPLCITKEQLDECTEIIVKTVKFF 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
   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 1LX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1LX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LX9)

(-) Gene Ontology  (7, 7)

Theoretical Model(hide GO term definitions)
Chain A   (OAT_PLAFD | Q07805)
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:0004587    ornithine-oxo-acid transaminase activity    Catalysis of the reaction: L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    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:0055129    L-proline biosynthetic process    The chemical reactions and pathways resulting in the formation of L-proline, an L-enantiomer of a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
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

Theoretical Model
  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
(no "Ligands, Modified Residues, Ions" information available for 1lx9)
 
  Sites
(no "Sites" information available for 1lx9)
 
  Cis Peptide Bonds
    Gly A:163 - Pro A:164   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model 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
  1lx9
    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
  OAT_PLAFD | Q07805
    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)
  2.6.1.13
    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
  OAT_PLAFD | Q07805
    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
        OAT_PLAFD | Q07805: 3lg0

(-) Related Entries Specified in the PDB File

2can HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH L-CANALINE
2oat ORNITHINE AMINOTRANSFERASE COMPLEXED WITH 5- FLUOROMETHYLORNITHINE