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

(-) Description

Title :  L-ALANINE DEHYDROGENASE
 
Authors :  P. J. Baker, Y. Sawa, H. Shibata, S. E. Sedelnikova, D. W. Rice
Date :  05 Jun 98  (Deposition) - 08 Jun 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Oxidoreductase, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Baker, Y. Sawa, H. Shibata, S. E. Sedelnikova, D. W. Rice
Analysis Of The Structure And Substrate Binding Of Phormidium Lapideum Alanine Dehydrogenase.
Nat. Struct. Biol. V. 5 561 1998
PubMed-ID: 9665169  |  Reference-DOI: 10.1038/817
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ALANINE DEHYDROGENASE
    Chains: A
    EC Number: 1.4.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: ALADH
    Expression System Plasmid: PNAD1
    Expression System Strain: MV1184
    Expression System Taxid: 562
    Expression System Vector: PUC18
    Gene: ALADH
    Organism Scientific: PHORMIDIUM LAPIDEUM
    Organism Taxid: 32060
    Other Details: MATSUE HOT SPRINGS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1PJB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PJB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PJB)

(-) 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:361
 aligned with O52942_PHOLP | O52942 from UniProtKB/TrEMBL  Length:361

    Alignment length:361
                                    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 
         O52942_PHOLP     1 MEIGVPKEIKNQEFRVGLSPSSVRTLVEAGHTVFIETQAGIGAGFADQDYVQAGAQVVPSAKDAWSREMVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETVELPNRSLPLLTPMSIIAGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGAQVQIFDINVERLSYLETLFGSRVELLYSNSAEIETAVAEADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEVFGVVHYGVPNMPGAVPWTATQALNNSTLPYVVKLANQGLKALETDDALAKGLNVQAHRLVHPAVQQVFPDLA 361
               SCOP domains d1pjba2 A:1-135,A:304-361 L-alanine dehydrogenase                                                                                      d1pjba1 A:136-303 L-alanine dehydrogenase                                                                                                                               d1pjba2 A:1-135,A:304-361 L-alanine dehydrogenase          SCOP domains
               CATH domains 1pjbA01 A:1-128,A:305-361  [code=3.40.50.1770, no name defined]                                                                 1pjbA02 A:129-304 NAD(P)-binding Rossmann-like Domain                                                                                                                           1pjbA01 A:1-128,A:305-361                                 CATH domains
               Pfam domains ---AlaDh_PNT_N-1pjbA01 A:4-136                                                                                                          -----------AlaDh_PNT_C-1pjbA02 A:148-296                                                                                                                        ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..............hhhhhhhh....eeeee....hhh...hhhhhhh..eee..hhhhh...eee......hhhhhh.....eeee...hhh.hhhhhhhhhh..eeeehhh...........hhhhhhhhhhhhhhhhhh..hhh................eeeee...hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh.eeee..hhhhhhhhhh..eeee..............hhhhhh.....eeee................hhh.eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pjb A   1 MEIGVPKEIKNQEFRVGLSPSSVRTLVEAGHTVFIETQAGIGAGFADQDYVQAGAQVVPSAKDAWSREMVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETVELPNRSLPLLTPMSIIAGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGAQVQIFDINVERLSYLETLFGSRVELLYSNSAEIETAVAEADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEVFGVVHYGVPNMPGAVPWTATQALNNSTLPYVVKLANQGLKALETDDALAKGLNVQAHRLVHPAVQQVFPDLA 361
                                    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
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Form_Glyc_dh (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (O52942_PHOLP | O52942)
molecular function
    GO:0000286    alanine dehydrogenase activity    Catalysis of the reaction: L-alanine + H2O + NAD+ = pyruvate + NH3 + NADH + H(+).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0042853    L-alanine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 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
(no "Ligands, Modified Residues, Ions" information available for 1pjb)
 
  Sites
(no "Sites" information available for 1pjb)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pjb)
 
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 | Biol. Unit 1 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
  1pjb
    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
  O52942_PHOLP | O52942
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.4.1.1
    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
  O52942_PHOLP | O52942
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O52942_PHOLP | O52942: 1pjc 1say

(-) Related Entries Specified in the PDB File

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