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

(-) Description

Title :  STRUCTURE OF BACILLUS HALMAPALUS ALPHA-AMYLASE, CRYSTALLIZED WITH THE SUBSTRATE ANALOGUE ACARBOSE AND MALTOSE
 
Authors :  L. Lyhne-Iversen, T. J. Hobley, S. G. Kaasgaard, P. Harris
Date :  31 Mar 06  (Deposition) - 05 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Amylase, Maltose Binding Site, Bacillus Halmapalus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lyhne-Iversen, T. J. Hobley, S. G. Kaasgaard, P. Harris
Structure Of Bacillus Halmapalus Alpha-Amylase Crystallized With And Without The Substrate Analogue Acarbose And Maltose.
Acta Crystallogr. , Sect. F V. 62 849 2006
PubMed-ID: 16946462  |  Reference-DOI: 10.1107/S174430910603096X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Organism Scientific: BACILLUS HALMAPALUS
    Organism Taxid: 79882

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA3Ligand/IonCALCIUM ION
3DAF2Ligand/Ion1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5-ENYL)AMINO)FRUCTOSE
4GLC6Ligand/IonALPHA-D-GLUCOSE
5MAL1Ligand/IonMALTOSE
6NA1Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:268 , ASN A:270 , TYR A:295 , GLC A:1491 , HOH A:1527BINDING SITE FOR RESIDUE BGC A 1490
02AC2SOFTWAREGLU A:194 , TYR A:198 , LYS A:239 , TRP A:268 , LEU A:340 , BGC A:1490 , DAF A:1492BINDING SITE FOR RESIDUE GLC A 1491
03AC3SOFTWARETRP A:15 , TYR A:58 , HIS A:107 , MET A:202 , ARG A:234 , ASP A:236 , ALA A:237 , LYS A:239 , HIS A:240 , GLU A:266 , HIS A:332 , ASP A:333 , GLC A:1491 , GLC A:1493BINDING SITE FOR RESIDUE DAF A 1492
04AC4SOFTWARETRP A:15 , MET A:202 , ASP A:333 , SER A:339 , DAF A:1492 , GLC A:1494 , HOH A:1663 , HOH A:1694 , HOH A:1698BINDING SITE FOR RESIDUE GLC A 1493
05AC5SOFTWAREMET A:202 , TYR A:203 , GLC A:1493 , GLC A:1495BINDING SITE FOR RESIDUE GLC A 1494
06AC6SOFTWAREASP A:166 , MET A:202 , TYR A:203 , GLC A:1494 , DAF A:1496 , HOH A:1640BINDING SITE FOR RESIDUE GLC A 1495
07AC7SOFTWARELYS A:72 , GLY A:110 , ALA A:111 , TRP A:140 , TRP A:167 , TYR A:203 , GLC A:1495 , HOH A:1547 , HOH A:1600 , HOH A:1615 , HOH A:1640 , HOH A:1681BINDING SITE FOR RESIDUE DAF A 1496
08AC8SOFTWAREASN A:128 , GLY A:304 , GLY A:305 , TRP A:347 , ASP A:432 , GLY A:433 , PRO A:434 , GLY A:476 , GLY A:477 , HOH A:1537 , HOH A:1540BINDING SITE FOR RESIDUE MAL A 1400
09AC9SOFTWARETRP A:439 , TRP A:469 , HOH A:1675BINDING SITE FOR RESIDUE GLC A 1300
10BC1SOFTWAREMET A:323 , TYR A:363 , HOH A:1576 , HOH A:1584 , HOH A:1670BINDING SITE FOR RESIDUE GLC A 1301
11BC2SOFTWAREASN A:106 , ASP A:199 , ASP A:205 , HIS A:240 , HOH A:1563BINDING SITE FOR RESIDUE CA A 1486
12BC3SOFTWAREASP A:163 , ALA A:186 , ASP A:188 , ASP A:207 , ASP A:209 , HOH A:1510BINDING SITE FOR RESIDUE CA A 1487
13BC4SOFTWAREGLY A:305 , TYR A:307 , HIS A:408 , ASN A:409 , ASP A:432 , HOH A:1548BINDING SITE FOR RESIDUE CA A 1488
14BC5SOFTWAREASP A:163 , ASP A:188 , ASP A:199 , ASP A:205 , VAL A:206BINDING SITE FOR RESIDUE NA A 1489

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:189 -Glu A:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GJP)

(-) 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:481
 aligned with AMT6_BACS7 | P19571 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:481
                                    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 
           AMT6_BACS7    38 TNGTMMQYFEWYLPNDGNHWNRLNSDASNLKSKGITAVWIPPAWKGASQNDVGYGAYDLYDLGEFNQKGTVRTKYGTRSQLQAAVTSLKNNGIQVYGDVVMNHKGGADATEMVRAVEVNPNNRNQEVTGEYTIEAWTRFDFPGRGNTHSSFKWRWYHFDGVDWDQSRRLNNRIYKFRGHGKAWDWEVDTENGNYDYLMYADIDMDHPEVVNELRNWGVWYTNTLGLDGFRIDAVKHIKYSFTRDWINHVRSATGKNMFAVAEFWKNDLGAIENYLQKTNWNHSVFDVPLHYNLYNASKSGGNYDMRNIFNGTVVQRHPSHAVTFVDNHDSQPEEALESFVEEWFKPLAYALTLTREQGYPSVFYGDYYGIPTHGVPAMRSKIDPILEARQKYAYGKQNDYLDHHNIIGWTREGNTAHPNSGLATIMSDGAGGSKWMFVGRNKAGQVWSDITGNRTGTVTINADGWGNFSVNGGSVSIWVNK 518
               SCOP domains d2gjpa2 A:5-395 automated matches                                                                                                                                                                                                                                                                                                                                                                      d2gjpa1 A:396-485 automated matches                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........hhhhhhhhhhhhhhhh...eeee....................................hhhhhhhhhhhhhhh..eeeeee...ee....eeeeeeeeeee..eeeee....eeeeeeee...............hhh.eeee...........eeee.......................eee...hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhhhhh.....hhhhh...hhhhhh...eeee................hhhhhhhhhhhhhhh...eeeeehhhhhh........hhhhhhhhhhhhhhh....eeee.....eeeeee..........eeeeee....eeeeee.hhhhh..eeee.......eee.....eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gjp A   5 TNGTMMQYFEWHLPNDGQHWNRLRDDASNLRNRGITAIWIPPAWKGTSQNDVGYGAYDLYDLGEFNQKGTVRTKYGTRSQLESAIHALKNNGVQVYGDVVMNHKGGADATENVLAVEVNPNNRNQEISGDYTIEAWTKFDFPGRGNTYSDFKWRWYHFDGVDWDQSRQFQNRIYKFRGDGKAWDWEVDSENGNYDYLMYADVDMDHPEVVNELRRWGEWYTNTLNLDGFRIDAVKHIKYSFTRDWLTHVRNATGKEMFAVAEFWKNDLGALENYLNKTNWNHSVFDVPLHYNLYNASNSGGNYDMAKLLNGTVVQKHPMHAVTFVDNHDSQPGESLESFVQEWFKPLAYALILTREQGYPSVFYGDYYGIPTHSVPAMKAKIDPILEARQNFAYGTQHDYFDHHNIIGWTREGNTTHPNSGLATIMSDGPGGEKWMYVGQNKAGQVWHDITGNKPGTVTINADGWANFSVNGGSVSIWVKR 485
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GJP)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMT6_BACS7 | P19571)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    GO:0033927    glucan 1,4-alpha-maltohexaosidase activity    Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in amylaceous polysaccharides, to remove successive maltohexaose residues from the non-reducing chain ends.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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.
    GO:0005983    starch catabolic process    The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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 ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DAF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:189 - Glu A:190   [ 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
  2gjp
    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
  AMT6_BACS7 | P19571
    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)
  3.2.1.1
    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
  AMT6_BACS7 | P19571
    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
        AMT6_BACS7 | P19571: 1wp6 1wpc 2d3l 2d3n 2gjr

(-) Related Entries Specified in the PDB File

1w9x CRYSTAL STRUCTURE OF BACILLUS HALMAPALUS ALPHA AMYLASE CRYSTALLIZED AT A DIFFERENT TEMPERATURE AND DIFFERENT RESOLUTION
2gjr CRYSTAL STRUCTURE THE SAME PROTEIN WITHOUT ANY SUBSTRATE ANALOGUES