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 :  GLYCOSIDE HYDROLASE FAMILY 77 4-ALPHA-GLUCANOTRANSFERASE FROM THERMUS BROCKIANUS
 
Authors :  S. -M. Yoon, J. -H. Jung, T. -Y. Jung, H. -N. Song, C. -S. Park, E. -J. Woo
Date :  28 Dec 09  (Deposition) - 27 Oct 10  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -H. Jung, T. -Y. Jung, D. Seo, S. -M. Yoon, H. Choi, B. C. Park, C. -S. Park, E. -J. Woo
Structural And Functional Analysis Of Substrate Recognition By The 250S Loop In Amylomaltase From Thermus Brockianus.
Proteins V. 79 633 2011
PubMed-ID: 21117235  |  Reference-DOI: 10.1002/PROT.22911

(-) Compounds

Molecule 1 - 4-ALPHA-GLUCANOTRANSFERASE
    Chains: A
    Organism Scientific: THERMUS BROCKIANUS
    Organism Taxid: 56956
    Strain: JCM11602
    Synonym: AMYLOMALTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1INS2Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
2PO41Ligand/IonPHOSPHATE ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:20 , GLY A:21 , ASP A:87 , PHE A:90 , PRO A:91 , ARG A:315 , HOH A:2004BINDING SITE FOR RESIDUE PO4 A1501
2AC2SOFTWAREVAL A:78 , VAL A:83 , ARG A:84BINDING SITE FOR RESIDUE SO4 A1502
3AC3SOFTWARECYS A:5 , ARG A:42BINDING SITE FOR RESIDUE INS A1503
4AC4SOFTWAREGLU A:27 , ARG A:30 , ARG A:34 , HOH A:2048BINDING SITE FOR RESIDUE INS A1504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X1I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X1I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X1I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X1I)

(-) Exons   (0, 0)

(no "Exon" information available for 2X1I)

(-) 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:497
 aligned with Q2VJA0_THEBO | Q2VJA0 from UniProtKB/TrEMBL  Length:500

    Alignment length:497
                                    13        23        33        43        53        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       
         Q2VJA0_THEBO     4 PCAYGLLLHPTSLPGPWGVGVLGEEARGFLRFLKEAGARYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLVDRGFVRLEDPGFPEGRVDYGLLYAWKWPALRAAFQGFRQKASPEEKEDFARFQEEEAWWLRDYALFMTLKSHHGGLPWNAWPLALRTREERALKEAEASLAEEIAFHAFTQWLFFRQWGALKEEAEALGIAFIGDMPIFVAEDSAEVWAHPEWFHLDEEGRPTVVAGVPPDYFSETGQRWGNPLYRWEVLEEEGFSFWIARLRKALELFHLVRIDHFRGFEAYWEIPASCPTAVEGRWVKAPGEKLFARIQEAFGRIPILAEDLGVITPEVEALRDRFGLPGMKVLQFAFDNGMENPFLPHNYPEHGRVVVYTGTHDNDTTLGWYRTATPHERDFLKRYLADWGITFREEAEVPWALMRLGMASRARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLRPGEIKEEHGERLLSLAEATGRV 500
               SCOP domains d2x1ia_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------Glyco_hydro_77-2x1iA01 A:11-497                                                                                                                                                                                                                                                                                                                                                                                                                                                                        --- Pfam domains
         Sec.struct. author ..eeeee.hhhhh.........hhhhhhhhhhhhhh...eee......................hhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhh..........eeeee.........eeeeee..hhhhhhhh.hhhhhhhhhhhh....eeeeehhhhh.eeeeee.........eeee.hhhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeee.hhh.........hhhhh.....eeee.......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeehhhhh..hhhhh....................hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x1i A   4 PCAYGLLLHPTSLPGPWGVGVLGEEARGFLRFLKEAGARYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLVDRGFVRLEDPGFPEGRVDYGLLYAWKWPALRAAFQGFRQKASPEEKEDFARFQEEEAWWLRDYALFMTLKSHHGGLPWNAWPLALRTREERALKEAEASLAEEIAFHAFTQWLFFRQWGALKEEAEALGIAFIGDMPIFVAEDSAEVWAHPEWFHLDEEGRPTVVAGVPPDYFSETGQRWGNPLYRWEVLEEEGFSFWIARLRKALELFHLVRIDHFRGFEAYWEIPASCPTAVEGRWVKAPGEKLFARIQEAFGRIPILAEDLGVITPEVEALRDRFGLPGMKVLQFAFDNGMENPFLPHNYPEHGRVVVYTGTHDNDTTLGWYRTATPHERDFLKRYLADWGITFREEAEVPWALMRLGMASRARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLRPGEIKEEHGERLLSLAEATGRV 500
                                    13        23        33        43        53        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
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X1I)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2VJA0_THEBO | Q2VJA0)
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.

 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
    INS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2x1i)
 

(-) 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
  2x1i
    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
  Q2VJA0_THEBO | Q2VJA0
    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)
  (no 'Enzyme Classificator' available)
    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
  Q2VJA0_THEBO | Q2VJA0
    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 2X1I)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2X1I)