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 - BETA CYCLODEXTRIN 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 :  21 Jul 15  (Deposition) - 04 Nov 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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
    Fragment: UNP RESIDUES 46-576
    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  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2EDO16Ligand/Ion1,2-ETHANEDIOL
3GLC2Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:261 , PHE A:265 , LYS A:268binding site for residue EDO A 603
02AC2SOFTWAREALA A:141 , ASN A:142 , MET A:294 , ARG A:359 , HOH A:701binding site for residue EDO A 604
03AC3SOFTWAREPRO A:295 , ILE A:296 , TYR A:297 , ASP A:373 , BGC A:601 , HOH A:818binding site for residue EDO A 605
04AC4SOFTWAREALA A:363 , TYR A:367 , ASP A:368 , GLU A:369 , CYS A:370 , LYS A:416binding site for residue EDO A 607
05AC5SOFTWAREASP A:220 , ARG A:246binding site for residue EDO A 608
06AC6SOFTWARETHR A:471 , HIS A:472 , ASN A:474 , THR A:476 , PRO A:523 , GLN A:525 , MET A:536binding site for residue EDO A 609
07AC7SOFTWARELEU A:87 , HIS A:472 , MET A:524 , GLN A:525 , MET A:536 , HOH A:738binding site for residue EDO A 610
08AC8SOFTWAREPHE B:261 , LEU B:264 , LYS B:268binding site for residue EDO B 603
09AC9SOFTWAREPRO B:295 , ILE B:296 , TYR B:297 , ASP B:373 , BGC B:601 , HOH B:811binding site for residue EDO B 604
10AD1SOFTWAREALA B:141 , ASN B:142 , ARG B:359binding site for residue EDO B 605
11AD2SOFTWAREGLN B:364 , TYR B:367 , ASP B:368 , GLU B:369 , ILE B:415 , LYS B:416binding site for residue EDO B 606
12AD3SOFTWAREASP B:220 , ARG B:246binding site for residue EDO B 607
13AD4SOFTWARETHR B:471 , HIS B:472 , ASN B:474 , THR B:476 , PRO B:523 , GLN B:525 , MET B:536 , EDO B:610 , HOH B:774binding site for residue EDO B 608
14AD5SOFTWARESER B:533 , ARG B:535 , THR B:538 , GLY B:544 , ASN B:545binding site for residue EDO B 609
15AD6SOFTWARELEU B:87 , MET B:524 , GLN B:525 , EDO B:608 , HOH B:723binding site for residue EDO B 610
16AD7SOFTWARESER A:134 , TYR A:136 , ALA A:137 , MET A:294 , ILE A:296 , ARG A:371 , ILE A:372 , HIS A:374 , PHE A:375 , GLU A:420 , HIS A:472 , ASP A:473 , ASN A:537 , PRO A:539 , ALA A:540 , EDO A:605 , HOH A:717binding site for Poly-Saccharide residues ASP A 373 through GLC A 602
17AD8SOFTWARESER A:134 , TYR A:136 , ALA A:137 , MET A:294 , ILE A:296 , ARG A:371 , ILE A:372 , HIS A:374 , PHE A:375 , GLU A:420 , HIS A:472 , ASP A:473 , ASN A:537 , PRO A:539 , ALA A:540 , EDO A:605 , HOH A:717 , SER B:134 , TYR B:136 , ALA B:137 , MET B:294 , ILE B:296 , ARG B:371 , ILE B:372 , HIS B:374 , PHE B:375 , GLU B:420 , HIS B:472 , ASP B:473 , ASN B:537 , PRO B:539 , ALA B:540 , EDO B:604 , HOH B:733binding site for Poly-Saccharide residues ASP B 373 through GLC B 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CPT)

(-) 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:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhh.eeeee.hhhhh.........hhhhhhhhhhhhhhh..eee......................hhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.........eeeee......eeeeee..hhhhhhh..hhhhhhhhhhhhhhh.eeeeehhhhh.eeeeee....hhhhheeee..hhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeee.hhh.........hhhhh...eeee.......hhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeehhhhh..hhhhh...................hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpt A  60 SVGEDFPSEYEQWLPVPDPESRRRAGVLLHPTSFRGPHGIGDLGEEAFRFIDWLHSTGCSVWQVLPLVPPDEGGSPYAGQDANCGNTLLISLDELVKDGLLIKDELPQPIDADSVNYQTANKLKSPLITKAAKRLIDGNGELKSKLLDFRNDPSISCWLEDAAYFAAIDNTLNAYSWFEWPEPLKNRHLSALEAIYESQKEFIDLFIAKQFLFQRQWQKVREYARRQGVDIMGDMPIYVGYHSADVWANKKHFLLNKKGFPLLVSGVPPSETGQLWGSPLYDWKAMESDQYSWWVNRIRRAQDLYDECRIDHFRGFAGFWAVPSEAKVAMVGRWKVGPGKSLFDAISKGVGKIKIIAEDLGVITKDVVELRKSIGAPGMAVLQFAFGGGADNPHLPHNHEVNQVVYSGTHDNDTIRGWWDTLDQEEKSKAMKYLSIAGEDDISWSVIQAAFSSTAQTAIIPMQDILGLGSSARMNTPATEVGNWGWRIPSSTSFDNLETESDRLRDLLSLYGRL 576
                                    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       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572    
                                                                                                                                                                                                                                                                                                      328|                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                       332                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhh.eeeee.hhhhh.........hhhhhhhhhhhhhh...eee......................hhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.........eeeee...eeeeee..hhhhhhh..hhhhhhhhhhhhhhh.eeeeehhhhh.eeeeee.........eeee..hhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeee.hhh.........hhhhh...eeee.......hhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeehhhhh..hhhhh...................hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpt B  60 SVGEDFPSEYEQWLPVPDPESRRRAGVLLHPTSFRGPHGIGDLGEEAFRFIDWLHSTGCSVWQVLPLVPPDEGGSPYAGQDANCGNTLLISLDELVKDGLLIKDELPQPIDADSVNYQTANKLKSPLITKAAKRLIDGNGELKSKLLDFRNDPSISCWLEDAAYFAAIDNTLNAYSWFEWPEPLKNRHLSALEAIYESQKEFIDLFIAKQFLFQRQWQKVREYARRQGVDIMGDMPIYVGYHSADVWANKKHFLLNKKGFPLLVSGVPPGQLWGSPLYDWKAMESDQYSWWVNRIRRAQDLYDECRIDHFRGFAGFWAVPSEAKVAMVGRWKVGPGKSLFDAISKGVGKIKIIAEDLGVITKDVVELRKSIGAPGMAVLQFAFGGGADNPHLPHNHEVNQVVYSGTHDNDTIRGWWDTLDQEEKSKAMKYLSIAGEDDISWSVIQAAFSSTAQTAIIPMQDILGLGSSARMNTPATEVGNWGWRIPSSTSFDNLETESDRLRDLLSLYGRL 576
                                    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       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575 
                                                                                                                                                                                                                                                                                                      328|                                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                       335
   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 5CPT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5cpt)
 

(-) 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
  5cpt
    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 5cq1 5csu 5csy

(-) Related Entries Specified in the PDB File

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