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 :  DISPROPORTIONATING ENZYME 1 FROM ARABIDOPSIS - ACARVIOSTATIN SOAK
 
Authors :  E. C. O'Neill, C. E. M. Stevenson, K. Tantanarat, D. Latousakis, M. I. Do M. Rejzek, T. Limpaseni, A. M. Smith, R. A. Field, D. M. Lawson
Date :  23 Jul 15  (Deposition) - 04 Nov 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Disproportionating Enzyme 1, 4-Alpha-Glucanotransferase, Glycoside Hydrolase Family 77, Starch Degradation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. C. O'Neill, C. E. Stevenson, K. Tantanarat, D. Latousakis, M. I. Donaldson, M. Rejzek, S. A. Nepogodiev, T. Limpaseni, R. A. Field D. M. Lawson
Structural Dissection Of The Maltodextrin Disproportionatio Cycle Of The Arabidopsis Plastidial Disproportionating Enzyme 1 (Dpe1).
J. Biol. Chem. V. 290 29834 2015
PubMed-ID: 26504082  |  Reference-DOI: 10.1074/JBC.M115.682245

(-) Compounds

Molecule 1 - 4-ALPHA-GLUCANOTRANSFERASE DPE1, CHLOROPLASTIC/AMYLOPLASTIC
    Chains: A, B
    EC Number: 2.4.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: DPE1, AT5G64860, MXK3.9
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: THE CRYSTALLISED PROTEIN CONTAINED RESIDUES 46-576 OF THE WILD-TYPE AMINO ACID SEQUENCE PRECEDED BY AN N-TERMINAL NICKEL AFFINITY TAG
    Synonym: AMYLOMALTASE,DISPROPORTIONATING ENZYME,D-ENZYME,PROTEIN DISPROPORTIONATING ENZYME 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1AGL4Ligand/Ion4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE
2BGC2Ligand/IonBETA-D-GLUCOSE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4GLC4Ligand/IonALPHA-D-GLUCOSE
5HMC4Ligand/Ion5-HYDROXYMETHYL-CHONDURITOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:363 , GLN A:364 , TYR A:367 , ASP A:368 , CYS A:370 , ILE A:415 , LYS A:416binding site for residue EDO A 602
2AC2SOFTWARESER B:533 , ARG B:535 , THR B:538 , GLY B:544 , ASN B:545binding site for residue EDO B 601
3AC3SOFTWARESER A:134 , TYR A:136 , ASP A:329 , LEU A:330 , PHE A:331 , GLN A:336 , LEU A:337 , TRP A:338 , GLY A:339 , ARG A:371 , ASP A:373 , HIS A:374 , GLU A:420 , LEU A:422 , GLY A:423 , PHE A:446 , HIS A:456 , HIS A:472 , ASP A:473 , ASN A:537 , PRO A:539 , ALA A:540 , THR A:541 , HOH A:720binding site for Poly-Saccharide residues HMC A 603 through BGC A 609
4AC4SOFTWARESER A:134 , TYR A:136 , ASP A:329 , LEU A:330 , PHE A:331 , GLN A:336 , LEU A:337 , TRP A:338 , GLY A:339 , ALA A:363 , GLN A:364 , TYR A:367 , ASP A:368 , CYS A:370 , ARG A:371 , ASP A:373 , HIS A:374 , ILE A:415 , LYS A:416 , GLU A:420 , LEU A:422 , GLY A:423 , PHE A:446 , HIS A:456 , HIS A:472 , ASP A:473 , ASN A:537 , PRO A:539 , ALA A:540 , THR A:541 , HOH A:720 , SER B:134 , TYR B:136 , ASP B:329 , LEU B:330 , PHE B:331 , GLN B:336 , LEU B:337 , TRP B:338 , ARG B:371 , ASP B:373 , HIS B:374 , GLU B:420 , LEU B:422 , GLY B:423 , PHE B:446 , HIS B:456 , HIS B:472 , ASP B:473 , ASN B:537 , PRO B:539 , ALA B:540 , THR B:541 , HOH B:705binding site for Poly-Saccharide residues HMC B 602 through BGC B 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CSU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CSU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CSU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CSU)

(-) Exons   (0, 0)

(no "Exon" information available for 5CSU)

(-) 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:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh.eeeee.hhhhh.........hhhhhhhhhhhhhhh..eee...........hhhhh......hhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh.........eeeee.........eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhh.eeeeee.........eeee..hhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeee.hhh.........hhhhh...eeee.......hhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhh....eeeeehhhhh..hhhhh...................hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5csu A  59 ISVGEDFPSEYEQWLPVPDPESRRRAGVLLHPTSFRGPHGIGDLGEEAFRFIDWLHSTGCSVWQVLPLVPPDEGGSPYAGQDANCGNTLLISLDELVKDGLLIKDELPQPIDADSVNYQTANKLKSPLITKAAKRLIDGNGELKSKLLDFRNDPSISCWLEDAAYFAAIDNTLNAYSWFEWPEPLKNRHLSALEAIYESQKEFIDLFIAKQFLFQRQWQKVREYARRQGVDIMGDMPIYVGYHSADVWANKKHFLLNKKGFPLLVSGVPPDLFSETGQLWGSPLYDWKAMESDQYSWWVNRIRRAQDLYDECRIDHFRGFAGFWAVPSEAKVAMVGRWKVGPGKSLFDAISKGVGKIKIIAEDLGVITKDVVELRKSIGAPGMAVLQFAFGGGADNPHLPHNHEVNQVVYSGTHDNDTIRGWWDTLDQEEKSKAMKYLSIAGEDDISWSVIQAAFSSTAQTAIIPMQDILGLGSSARMNTPATEVGNWGWRIPSSTSFDNLETESDRLRDLLSLYGRL 576
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568        


Chain B from PDB  Type:PROTEIN  Length:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh.eeeee.hhhhh.........hhhhhhhhhhhhhhh..eee...........hhhhh......hhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh.........eeeee.........eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhh.eeeeee.........eeee..hhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeee.hhh.........hhhhh...eeee.......hhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhh....eeeeehhhhh..hhhhh...................hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5csu B  59 ISVGEDFPSEYEQWLPVPDPESRRRAGVLLHPTSFRGPHGIGDLGEEAFRFIDWLHSTGCSVWQVLPLVPPDEGGSPYAGQDANCGNTLLISLDELVKDGLLIKDELPQPIDADSVNYQTANKLKSPLITKAAKRLIDGNGELKSKLLDFRNDPSISCWLEDAAYFAAIDNTLNAYSWFEWPEPLKNRHLSALEAIYESQKEFIDLFIAKQFLFQRQWQKVREYARRQGVDIMGDMPIYVGYHSADVWANKKHFLLNKKGFPLLVSGVPPDLFSETGQLWGSPLYDWKAMESDQYSWWVNRIRRAQDLYDECRIDHFRGFAGFWAVPSEAKVAMVGRWKVGPGKSLFDAISKGVGKIKIIAEDLGVITKDVVELRKSIGAPGMAVLQFAFGGGADNPHLPHNHEVNQVVYSGTHDNDTIRGWWDTLDQEEKSKAMKYLSIAGEDDISWSVIQAAFSSTAQTAIIPMQDILGLGSSARMNTPATEVGNWGWRIPSSTSFDNLETESDRLRDLLSLYGRL 576
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568
   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 5CSU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CSU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CSU)

(-) Gene Ontology  (11, 11)

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
    AGL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HMC  [ 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
(no "Cis Peptide Bonds" information available for 5csu)
 

(-) 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
  5csu
    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
  DPE1_ARATH | Q9LV91
    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)
  2.4.1.25
    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
  DPE1_ARATH | Q9LV91
    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
        DPE1_ARATH | Q9LV91: 5cpq 5cps 5cpt 5cq1 5csy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CSU)