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 :  STRUCTURE OF MOUSE 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (ALDH4A1) COMPLEXED WITH SUCCINATE
 
Authors :  T. A. Pemberton, J. J. Tanner
Date :  30 Jun 13  (Deposition) - 28 Aug 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Proline Catabolism, Substrate Recognition, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Pemberton, J. J. Tanner
Structural Basis Of Substrate Selectivity Of Delta (1)-Pyrroline-5-Carboxylate Dehydrogenase (Aldh4A1): Semialdehyde Chain Length.
Arch. Biochem. Biophys. V. 538 34 2013
PubMed-ID: 23928095  |  Reference-DOI: 10.1016/J.ABB.2013.07.024

(-) Compounds

Molecule 1 - DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE, MITOCHONDRIAL
    Chains: A, B
    EC Number: 1.5.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 21-562
    Gene: ADLH4A1, ALDH4A1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: P5C DEHYDROGENASE, ALDEHYDE DEHYDROGENASE FAMILY 4 MEMBER A1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2SIN2Ligand/IonSUCCINIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:63 , TRP A:74 , TYR A:80 , LYS A:93 , THR B:61 , HOH B:710 , HOH B:1046BINDING SITE FOR RESIDUE 1PE A 601
2AC2SOFTWAREASN A:211 , PHE A:212 , LYS A:347 , CYS A:348 , SER A:349 , GLY A:512 , SER A:513 , PHE A:520 , HOH A:1007 , HOH A:1009BINDING SITE FOR RESIDUE SIN A 602
3AC3SOFTWARETHR A:61 , HOH A:711 , HOH A:889 , HOH A:1053 , HOH A:1081 , ALA B:63 , TRP B:74 , TYR B:80 , LYS B:93BINDING SITE FOR RESIDUE 1PE B 601
4AC4SOFTWAREASN B:211 , PHE B:212 , LYS B:347 , CYS B:348 , SER B:349 , GLY B:512 , SER B:513 , PHE B:520 , HOH B:1013 , HOH B:1014BINDING SITE FOR RESIDUE SIN B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LH2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:189 -Pro A:190
2Pro B:189 -Pro B:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LH2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LH2)

(-) Exons   (0, 0)

(no "Exon" information available for 4LH2)

(-) 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:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4lh2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh...ee..eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee......eeeee....hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh......eee...hhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhh....eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh..eeeee...ee.....ee..eeeee....hhhhh......eeeeeeehhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhh.....eeee................ee...........hhhhhhh..eeeeee........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lh2 A  30 LKVANEPILAFSQGSPERDALQKALKDLKGQTEAIPCVVGDEEVWTSDIQYQLSPFNHAHKVAKFCYADKALLNRAIDAALAARKEWDLKPMADRAQVFLKAADMLSGPRRAEVLAKTMVGQGKTVIQAEIDAAAELIDFFRFNAKFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISPFNFTAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTFGDTVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADVDSVVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKAFARIKKWLEHARSSPSLSILAGGQCNESVGYYVEPCIIESKDPQEPIMKEEIFGPVLTVYVYPDDKYRETLKLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKSTGSVVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWRYSYMQ 563
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559    


Chain B from PDB  Type:PROTEIN  Length:544
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4lh2b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhh...ee..eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee......eeeee....hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh......eee...hhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhh....eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhh..eeeee...ee.....ee..eeeee....hhhhh......eeeeeeehhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhh.....eeee................ee...........hhhhhhh..eeeeee........hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lh2 B  20 HMLRWKHTSSLKVANEPILAFSQGSPERDALQKALKDLKGQTEAIPCVVGDEEVWTSDIQYQLSPFNHAHKVAKFCYADKALLNRAIDAALAARKEWDLKPMADRAQVFLKAADMLSGPRRAEVLAKTMVGQGKTVIQAEIDAAAELIDFFRFNAKFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISPFNFTAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTFGDTVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADVDSVVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKAFARIKKWLEHARSSPSLSILAGGQCNESVGYYVEPCIIESKDPQEPIMKEEIFGPVLTVYVYPDDKYRETLKLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAAGNFYINDKSTGSVVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWRYSYMQ 563
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559
   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  (0, 0)

(no "CATH Domain" information available for 4LH2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LH2)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:189 - Pro A:190   [ RasMol ]  
    Pro B:189 - Pro B:190   [ 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
  4lh2
    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
  AL4A1_MOUSE | Q8CHT0
    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)
  1.5.1.12
    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
  AL4A1_MOUSE | Q8CHT0
    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
        AL4A1_MOUSE | Q8CHT0: 3v9j 3v9k 3v9l 4e3x 4lgz 4lh0 4lh1 4lh3

(-) Related Entries Specified in the PDB File

3v9g 3v9h 3v9i 3v9j 3v9k 3v9l 4lgz 4lh0 4lh1 4lh3