Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE DETERMINATION AND REFINEMENT AT 1.8 A RESOLUTION OF DISPROPORTIONATING ENZYME FROM POTATO
 
Authors :  K. Imamura, T. Matsuura, T. Takaha, K. Fujii, A. Nakagawa, M. Kusunoki,
Date :  08 Apr 05  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Disproportionating Enzyme, Amylomaltase, D-Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Imamura, T. Matsuura, T. Takaha, K. Fujii, A. Nakagawa, M. Kusunoki Y. Nitta
Structure Determination And Refinement At 1. 8 A Resolution Of Disproportionating Enzyme From Potato
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 4-ALPHA-GLUCANOTRANSFERASE
    Chains: A
    EC Number: 2.4.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Synonym: DISPROPORTIONATING ENZYME, AMYLOMALTASE, D-ENZYME
    Tissue: TUBER

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL9Ligand/IonGLYCEROL
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL9Ligand/IonGLYCEROL
Biological Unit 2 (1, 18)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL18Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:180 , HOH A:2002 , HOH A:2044 , HOH A:2059 , HOH A:2087 , HOH A:2258 , HOH A:2290BINDING SITE FOR RESIDUE CA A 2001
02AC2SOFTWAREHIS A:420 , ASP A:421 , ASN A:485 , HOH A:2381 , HOH A:2470 , HOH A:2500BINDING SITE FOR RESIDUE GOL A 1001
03AC3SOFTWAREPRO A:243 , ILE A:244 , TYR A:245 , TRP A:286 , ASP A:321 , HOH A:2541BINDING SITE FOR RESIDUE GOL A 1002
04AC4SOFTWAREGLY A:371 , PHE A:394 , HIS A:404BINDING SITE FOR RESIDUE GOL A 1003
05AC5SOFTWAREGLY A:77 , ASP A:80 , ASP A:104 , ASP A:105 , LEU A:149 , HOH A:2333 , HOH A:2394 , HOH A:2652BINDING SITE FOR RESIDUE GOL A 1004
06AC6SOFTWARETYR A:41 , GLU A:100 , MET A:110 , THR A:181 , ILE A:182 , SER A:183 , ASP A:186 , HOH A:2422 , HOH A:2556 , HOH A:2651BINDING SITE FOR RESIDUE GOL A 1005
07AC7SOFTWAREASP A:168 , TYR A:171 , ARG A:194 , LEU A:196 , HOH A:2551BINDING SITE FOR RESIDUE GOL A 1006
08AC8SOFTWAREARG A:426 , SER A:453 , ARG A:454 , ASP A:474 , GLY A:477 , LYS A:513 , HOH A:2092 , HOH A:2222 , HOH A:2240BINDING SITE FOR RESIDUE GOL A 1007
09AC9SOFTWAREASP A:505 , ASP A:508 , HOH A:2489BINDING SITE FOR RESIDUE GOL A 1008
10BC1SOFTWARESER A:163 , SER A:164 , ASP A:168 , HOH A:2251 , HOH A:2429 , HOH A:2663BINDING SITE FOR RESIDUE GOL A 1009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X1N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X1N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X1N)

(-) Exons   (0, 0)

(no "Exon" information available for 1X1N)

(-) 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:523
 aligned with DPEP_SOLTU | Q06801 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:523
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573   
           DPEP_SOLTU    54 VPAVGEDFPIDYADWLPKRDPNDRRRAGILLHPTSFPGPYGIGDLGPQAFKFLDWLHLAGCSLWQVLPLVPPGKRGNEDGSPYSGQDANCGNTLLISLEELVDDGLLKMEELPEPLPTDRVNYSTISEIKDPLITKAAKRLLSSEGELKDQLENFRRDPNISSWLEDAAYFAAIDNSVNTISWYDWPEPLKNRHLAALEEVYQSEKDFIDIFIAQQFLFQRQWKKVRDYARSKGISIMGDMPIYVGYHSADVWANKKQFLLNRKGFPLIVSGVPPDAFSETGQLWGSPLYDWKAMEKDGFSWWVRRIQRATDLFDEFRIDHFRGFAGFWAVPSEEKIAILGRWKVGPGKPLFDAILQAVGKINIIAEDLGVITEDVVQLRKSIEAPGMAVLQFAFGSDAENPHLPHNHEQNQVVYTGTHDNDTIRGWWDTLPQEEKSNVLKYLSNIEEEEISRGLIEGAVSSVARIAIIPMQDVLGLGSDSRMNIPATQFGNWSWRIPSSTSFDNLDAEAKKLRDILATYGRL 576
               SCOP domains d1x1na1 A:2-524 Amylomaltase MalQ                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------1x1nA01 A:22-524 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------Glyco_hydro_77-1x1nA01 A:32-521                                                                                                                                                                                                                                                                                                                                                                                                                                                                           --- Pfam domains
         Sec.struct. author ..........hhhhh....hhhhh.eeeee.hhhhh.........hhhhhhhhhhhhhhh..eee..........................hhhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.........eeee..................hhhhhhhh.hhhhhhhhhhhhhhh.eeeeehhhhh.eeeeee.........eeee..hhhhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee.hhh.........hhhhh...eeee.......hhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhh....eeeeehhhhh..hhhhh...................hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1n A   2 VPAVGEDFPIDYADWLPKRDPNDRRRAGILLHPTSFPGPYGIGDLGPQAFKFLDWLHLAGCSLWQVLPLVPPGKRGNEDGSPYSGQDANCGNTLLISLEELVDDGLLKMEELPEPLPTDRVNYSTISEIKDPLITKAAKRLLSSEGELKDQLENFRRDPNISSWLEDAAYFAAIDNSVNTISWYDWPEPLKNRHLAALEEVYQSEKDFIDIFIAQQFLFQRQWKKVRDYARSKGISIMGDMPIYVGYHSADVWANKKQFLLNRKGFPLIVSGVPPDAFSETGQLWGSPLYDWKAMEKDGFSWWVRRIQRATDLFDEFRIDHFRGFAGFWAVPSEEKIAILGRWKVGPGKPLFDAILQAVGKINIIAEDLGVITEDVVQLRKSIEAPGMAVLQFAFGSDAENPHLPHNHEQNQVVYTGTHDNDTIRGWWDTLPQEEKSNVLKYLSNIEEEEISRGLIEGAVSSVARIAIIPMQDVLGLGSDSRMNIPATQFGNWSWRIPSSTSFDNLDAEAKKLRDILATYGRL 524
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (DPEP_SOLTU | Q06801)
molecular function
    GO:0004134    4-alpha-glucanotransferase activity    Catalysis of the transfer of a segment of a (1->4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1->4)-alpha-D-glucan.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0005977    glycogen metabolic process    The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
cellular component
    GO:0009501    amyloplast    A plastid whose main function is to synthesize and store starch.
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1x1n)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  1x1n
    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
  DPEP_SOLTU | Q06801
    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
  DPEP_SOLTU | Q06801
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1X1N)

(-) Related Entries Specified in the PDB File

1ww0 THE SAME PROTEIN LABELED WITH SELENO-METHIONIN