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 :  SUGAR BEET ALPHA-GLUCOSIDASE WITH ACARVIOSYL-MALTOHEXAOSE
 
Authors :  T. Tagami, K. Yamashita, M. Okuyama, H. Mori, M. Yao, A. Kimura
Date :  09 Jul 13  (Deposition) - 16 Jul 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Glucosidase, Glycoside Hydrolase Family 31, (Beta/Alpha)8- Barrel, Acarbose Derivative, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tagami, K. Yamashita, M. Okuyama, H. Mori, M. Yao, A. Kimura
Structural Advantage Of Sugar Beet Alpha-Glucosidase To Stabilize The Michaelis Complex With Long-Chain Substrate
J. Biol. Chem. V. 290 1796 2014
PubMed-ID: 25451917  |  Reference-DOI: 10.1074/JBC.M114.606939

(-) Compounds

Molecule 1 - ALPHA-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.20
    Organism Common: SUGAR BEET
    Organism Scientific: BETA VULGARIS
    Organism Taxid: 161934
    Other Details: SEEDS
    Strain: CV. ABEND

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1ACR1Ligand/IonALPHA-ACARBOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3GLC4Ligand/IonALPHA-D-GLUCOSE
4GOL1Ligand/IonGLYCEROL
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:728 , TYR A:729 , HOH A:1456 , HOH A:1895 , HOH A:2091BINDING SITE FOR RESIDUE GOL A 1012
2AC2SOFTWAREGLU A:301 , ARG A:670 , ARG A:676 , ARG A:699 , HOH A:1250 , HOH A:1265 , HOH A:1611 , HOH A:1960 , HOH A:2110 , HOH A:2120BINDING SITE FOR RESIDUE SO4 A 1013
3AC3SOFTWAREASN A:404 , SER A:406 , LYS A:903 , HOH A:1350 , HOH A:1525 , HOH A:1831 , HOH A:1984 , HOH A:1992 , HOH A:1994 , HOH A:2002BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 404 RESIDUES 1006 TO 1008
4AC4SOFTWAREASN A:728 , SER A:731 , HOH A:1545 , HOH A:1826 , HOH A:1905BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 728 RESIDUES 1010 TO 1011
5AC5SOFTWAREILE A:821 , ASN A:822 , ASN A:823 , THR A:825 , GLU A:905 , HOH A:1658 , HOH A:2079BINDING SITE FOR MONO-SACCHARIDE NAG A1009 BOUND TO ASN A 823
6AC6SOFTWAREASP A:232 , ILE A:233 , ALA A:234 , PHE A:236 , ASN A:237 , LEU A:240 , TRP A:329 , ASP A:357 , ILE A:358 , ARG A:388 , ASN A:389 , ILE A:396 , TRP A:467 , ASP A:469 , MET A:470 , SER A:497 , GLY A:499 , ARG A:500 , VAL A:501 , PRO A:502 , ARG A:552 , TRP A:565 , ASP A:568 , PHE A:601 , HIS A:626 , THR A:768 , SER A:838 , GLN A:839 , ARG A:840 , HOH A:1102 , HOH A:1107 , HOH A:1289 , HOH A:1439 , HOH A:1502 , HOH A:1619 , HOH A:1620 , HOH A:1693 , HOH A:1873 , HOH A:1932 , HOH A:2026 , HOH A:2034 , HOH A:2037 , HOH A:2043 , HOH A:2066BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1001 TO 1005

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:599 -A:610

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr A:158 -Pro A:159
2Gly A:211 -Glu A:212
3Ser A:255 -Pro A:256
4Gly A:297 -Arg A:298
5Glu A:472 -Ala A:473

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WEO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WEO)

(-) Exons   (0, 0)

(no "Exon" information available for 3WEO)

(-) 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:827
 aligned with L0N7E5_BETVU | L0N7E5 from UniProtKB/TrEMBL  Length:913

    Alignment length:872
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907  
         L0N7E5_BETVU    38 GEAIGYGYQVKNAKVDNSTGKSLTALLQLIRNSPVYGPDIQFLSFTASFEEDDTLRIRITDANNRRWEIPNEVLPRPPPPPSPPPLSSLQHLPKPIPQNQPTTTVLSHPHSDLVFTLFHTTPFGFTIYRKSTHDVLFDATPIPSNPTTFLIYKDQYLQLSSSLPAQQAHLYGLGEHTKPTFQLAHNQILTLWNADIASFNRDLNLYGSHPFYMDVRSSPMVGSTHGVFLLNSNGMDVEYTGDRITYKVIGGIIDLYIFAGRTPEMVLDQYTKLIGRPAPMPYWAFGFHQCRWGYRDVNEIETVVDKYAEARIPLEVMWTDIDYMDAFKDFTLDPVHFPLDKMQQFVTKLHRNGQRYVPILDPGINTNKSYGTFIRGMQSNVFIKRDGNPYLGSVWPGPVYYPDFLDPAARSFWVDEIKRFRDILPIDGIWIDMNEASNFITSAPTPGSTLDNPPYKINNSGGRVPINSKTIPATAMHYGNVTEYNAHNLYGFLESQATREALVRTSNERPFLLSRSTFAGSGKYTAHWTGDNAARWDDLQYSIPTMLNFGLFGMPMIGADICGFAESTTEELCRRWIQLGAFYPFSRDHSARDTTHQELYLWESVAASARTVLGLRYQLLPYYYTLMYDANLRGIPIARPLFFTFPDDVATYGISSQFLIGRGIMVSPVLQPGAVSVNAYFPRGNWFSLFNYTSSVSVSAGTYVSLSAPPDHINVHIHEGNIVAMQGEAMTTQAARSTPFHLLVVMSDHVASTGELFLDNGIEMDIGGPGGKWTLVRFFAESGINNLTISSEVVNRGYAMSQRWVMDKITILGLKRRVRIKEYTVQKDAGAIKIKGLGLRTSSHNQGGFVVSVISDLRQLVGQAFKLELEFE 909
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee......eeeeeeee............eeeeeeeeee..eeeeeeee....................-------------------..eeee......eeeeee.....eeeeee.....eeee......hhhhh.eee..eeeeeee.....eeeeeee............eeeee.................eeeeeeee......eeeeeee.....eeeee...eeeeee....eeeeee...hhhhhhhhhhhhhh.....hhhhhh.ee......hhhhhhhhhhhhhhh.....eeeehhhhh.............hhhhhhhhhhhhhhh..eeeeee...ee....hhhhhhhhhh....ee..ee..eee..eeee.....hhhhhhhhhhhhhhhhhhh....eee..........................hhhhh.............ee...eehhhhh.hhhhhhhhhhhhhhhhhh.....eee.....hhhhh.eee......hhhhhhhhhhhhhhhhhh....ee.ee.......hhhhhhhhhhhhh.....ee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhh..hhhhh.....eee...eeee........eeeeee..eeeee..eeeeeeee...eeeeee......eeeee...eeee.....hhhhhhh..eeeeee......eeeeeee...............eeeeeeeee...eeeeeeeeehhhhhhhh..eeeeeeeeee...eee.--------------------------..eeeee....ee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3weo A  38 GEAIGYGYQVKNAKVDNSTGKSLTALLQLIRNSPVYGPDIQFLSFTASFEEDDTLRIRITDANNRRWEIPNEVLPRPPPPP-------------------PTTTVLSHPHSDLVFTLFHTTPFGFTIYRKSTHDVLFDATPIPSNPTTFLIYKDQYLQLSSSLPAQQAHLYGLGEHTKPTFQLAHNQILTLWNADIASFNRDLNLYGSHPFYMDVRSSPMVGSTHGVFLLNSNGMDVEYTGDRITYKVIGGIIDLYIFAGRTPEMVLDQYTKLIGRPAPMPYWAFGFHQCRWGYRDVNEIETVVDKYAEARIPLEVMWTDIDYMDAFKDFTLDPVHFPLDKMQQFVTKLHRNGQRYVPILDPGINTNKSYGTFIRGMQSNVFIKRDGNPYLGSVWPGPVYYPDFLDPAARSFWVDEIKRFRDILPIDGIWIDMNEASNFITSAPTPGSTLDNPPYKINNSGGRVPINSKTIPATAMHYGNVTEYNAHNLYGFLESQATREALVRTSNERPFLLSRSTFAGSGKYTAHWTGDNAARWDDLQYSIPTMLNFGLFGMPMIGADICGFAESTTEELCRRWIQLGAFYPFSRDHSARDTTHQELYLWESVAASARTVLGLRYQLLPYYYTLMYDANLRGIPIARPLFFTFPDDVATYGISSQFLIGRGIMVSPVLQPGAVSVNAYFPRGNWFSLFNYTSSVSVSAGTYVSLSAPPDHINVHIHEGNIVAMQGEAMTTQAARSTPFHLLVVMSDHVASTGELFLDNGIEMDIGGPGGKWTLVRFFAESGINNLTISSEVVNRGYAMSQRWVMDKITILGLKRRVRIK--------------------------GFVVSVISDLRQLVGQAFKLELEFE 909
                                    47        57        67        77        87        97       107       117|        -         -|      147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857|        -         -       887       897       907  
                                                                                                          118                 138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             858                        885
   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 3WEO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WEO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WEO)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (L0N7E5_BETVU | L0N7E5)
molecular function
    GO:0004558    alpha-1,4-glucosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-(1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0032450    maltose alpha-glucosidase activity    Catalysis of the reaction: alpha-maltose + H2O = 2 alpha-D-glucose.
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:0000023    maltose metabolic process    The chemical reactions and pathways involving the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose), an intermediate in the catabolism of glycogen and starch.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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
    ACR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Glu A:472 - Ala A:473   [ RasMol ]  
    Gly A:211 - Glu A:212   [ RasMol ]  
    Gly A:297 - Arg A:298   [ RasMol ]  
    Ser A:255 - Pro A:256   [ RasMol ]  
    Thr A:158 - Pro A:159   [ 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
  3weo
    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
  L0N7E5_BETVU | L0N7E5
    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)
  3.2.1.20
    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
  L0N7E5_BETVU | L0N7E5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        L0N7E5_BETVU | L0N7E5: 3w37 3w38 3wel 3wem 3wen

(-) Related Entries Specified in the PDB File

3w37 THE SAME PROTEIN COMPLEXED WITH ACARBOSE (AC4)
3w38 LIGAND-FREE FORM OF THE SAME PROTEIN
3wel THE SAME PROTEIN COMPLEXED WITH ACARVIOSYL-MALTOTRIOSE (AC5)
3wem THE SAME PROTEIN COMPLEXED WITH ACARVIOSYL-MALTOTETRAOSE (AC6)
3wen THE SAME PROTEIN COMPLEXED WITH ACARVIOSYL-MALTOPENTAOSE (AC7)