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 :  CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1 (TVAI) MUTANT D356N/E396Q COMPLEXED WITH P5, A PULLULAN MODEL OLIGOSACCHARIDE
 
Authors :  A. Abe, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Date :  02 Aug 05  (Deposition) - 11 Jul 06  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Amylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Abe, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Complexes Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 And Pullulan Model Oligossacharides Provide New Insight Into The Mechanism For Recognizing Substrates With Alpha-(1, 6) Glycosidic Linkages
Febs J. V. 272 6145 2005
PubMed-ID: 16302977  |  Reference-DOI: 10.1111/J.1742-4658.2005.05013.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE I
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: THERMOACTINOMYCES VULGARIS
    Organism Taxid: 2026
    Strain: R-47
    Synonym: TVA I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric/Biological Unit (4, 23)
No.NameCountTypeFull Name
1BGC10Ligand/IonBETA-D-GLUCOSE
2CA3Ligand/IonCALCIUM ION
3GLC9Ligand/IonALPHA-D-GLUCOSE
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:529 , GLC A:702 , HOH A:2471BINDING SITE FOR RESIDUE BGC A 701
02AC2SOFTWARETHR A:606 , BGC A:701 , BGC A:703 , HOH A:2159 , HOH A:2200 , HOH A:2471BINDING SITE FOR RESIDUE GLC A 702
03AC3SOFTWARETYR A:174 , ALA A:515 , ASP A:516 , PRO A:517 , ASP A:518 , GLC A:702 , BGC A:704 , HOH A:2438BINDING SITE FOR RESIDUE BGC A 703
04AC4SOFTWAREGLN A:547 , ASN A:577 , GLN A:637 , BGC A:703 , GLC A:705 , HOH A:2198 , HOH A:2244BINDING SITE FOR RESIDUE BGC A 704
05AC5SOFTWAREPRO A:549 , VAL A:576 , ASN A:577 , BGC A:704 , GLC A:706 , HOH A:2116 , HOH A:2308 , HOH A:2309 , HOH A:2340BINDING SITE FOR RESIDUE GLC A 705
06AC6SOFTWARESER A:182 , ASP A:516 , GLC A:705 , GLC A:707 , HOH A:2176 , HOH A:2308BINDING SITE FOR RESIDUE GLC A 706
07AC7SOFTWAREHIS A:221 , TYR A:223 , ASP A:516 , ARG A:520 , GLC A:706 , GLC A:708 , HOH A:2376BINDING SITE FOR RESIDUE GLC A 707
08AC8SOFTWARETYR A:223 , HIS A:267 , PHE A:310 , ARG A:354 , ASN A:356 , GLN A:396 , HIS A:471 , ASP A:472 , GLC A:707 , GLC A:709BINDING SITE FOR RESIDUE GLC A 708
09AC9SOFTWAREPHE A:310 , TYR A:360 , GLN A:396 , TRP A:398 , GLC A:708 , GLC A:710 , HOH A:2254BINDING SITE FOR RESIDUE GLC A 709
10BC1SOFTWARETRP A:398 , GLN A:434 , ASP A:472 , GLC A:709BINDING SITE FOR RESIDUE GLC A 710
11BC2SOFTWAREALA A:115 , ASP A:116 , ASP A:117 , TYR A:119 , ASN A:402 , BGC A:802 , HOH A:2084BINDING SITE FOR RESIDUE BGC A 801
12BC3SOFTWAREPHE A:58 , TYR A:89 , ARG A:91 , ASP A:117 , BGC A:801BINDING SITE FOR RESIDUE BGC A 802
13BC4SOFTWAREASP A:418 , TRP A:448BINDING SITE FOR RESIDUE GLC A 810
14BC5SOFTWAREASP A:66 , SER A:67 , BGC A:902 , HOH A:2337BINDING SITE FOR RESIDUE GLC A 901
15BC6SOFTWARETRP A:65 , ASP A:66 , GLC A:901 , BGC A:903BINDING SITE FOR RESIDUE BGC A 902
16BC7SOFTWAREBGC A:902 , BGC A:904 , HOH A:2172BINDING SITE FOR RESIDUE BGC A 903
17BC8SOFTWAREGLY A:41 , ILE A:43 , TRP A:65 , ASP A:75 , BGC A:903 , BGC A:905 , HOH A:2184 , HOH A:2241 , HOH A:2364BINDING SITE FOR RESIDUE BGC A 904
18BC9SOFTWARELYS A:40 , TRP A:65 , ASN A:68 , ASP A:75 , BGC A:904BINDING SITE FOR RESIDUE BGC A 905
19CC1SOFTWAREASP A:483 , TRP A:485 , GLY A:629 , HIS A:630BINDING SITE FOR RESIDUE BGC A 910
20CC2SOFTWAREALA A:2 , ASP A:4 , ASN A:6 , ASP A:42 , ASP A:96 , HOH A:2474BINDING SITE FOR RESIDUE CA A 2001
21CC3SOFTWAREASN A:145 , ASP A:147 , ASN A:150 , ASP A:151 , GLY A:187 , ASP A:189 , HOH A:2118BINDING SITE FOR RESIDUE CA A 2002
22CC4SOFTWAREASP A:276 , ASN A:279 , PHE A:281 , SER A:283 , GLU A:288 , HOH A:2263BINDING SITE FOR RESIDUE CA A 2003
23CC5SOFTWAREASP A:446 , LEU A:559 , THR A:561 , HOH A:2058BINDING SITE FOR RESIDUE MPD A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D0G)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:303 -Pro A:304
2Pro A:346 -Pro A:347
3Asp A:516 -Pro A:517

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D0G)

(-) Exons   (0, 0)

(no "Exon" information available for 2D0G)

(-) 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:637
 aligned with NEPU1_THEVU | Q60053 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:637
                                    39        49        59        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       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       
          NEPU1_THEVU    30 AANDNNVEWNGLFHDQGPLFDNAPEPTSTQSVTLKLRTFKGDITSANIKYWDTADNAFHWVPMVWDSNDPTGTFDYWKGTIPASPSIKYYRFQINDGTSTAWYNGNGPSSTEPNADDFYIIPNFKTPDWLKNGVMYQIFPDRFYNGDSSNDVQTGSYTYNGTPTEKKAWGSSVYADPGYDNSLVFFGGDLAGIDQKLGYIKKTLGANILYLNPIFKAPTNHKYDTQDYMAVDPAFGDNSTLQTLINDIHSTANGPKGYLILDGVFNHTGDSHPWFDKYNNFSSQGAYESQSSPWYNYYTFYTWPDSYASFLGFNSLPKLNYGNSGSAVRGVIYNNSNSVAKTYLNPPYSVDGWRLDAAQYVDANGNNGSDVTNHQIWSEFRNAVKGVNSNAAIIGEYWGNANPWTAQGNQWDAATNFDGFTQPVSEWITGKDYQNNSASISTTQFDSWLRGTRANYPTNVQQSMMNFLSNHDITRFATRSGGDLWKTYLALIFQMTYVGTPTIYYGDEYGMQGGADPDNRRSFDWSQATPSNSAVALTQKLITIRNQYPALRTGSFMTLITDDTNKIYSYGRFDNVNRIAVVLNNDSVSHTVNVPVWQLSMPNGSTVTDKITGHSYTVQNGMVTVAVDGHYGAVLAQ 666
               SCOP domains d2d0ga1 A:1-122 Maltogenic amylase, N-terminal domain N                                                                   d2d0ga3 A:123-554 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                                                                            d2d0ga2 A:555-637 Maltogenic amylase                                                SCOP domains
               CATH domains 2d0gA01 A:1-124 Immunoglobulins                                                                                             2d0gA02 A:125-547 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                         2d0gA03 A:548-637 Golgi alpha-mannosidase II                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................eeeeeeee.....eeeeeeee.....eeeee.eeeee.....eeeeeeee......eeeeeeeee..eeeeee..eee........eee......hhhhhhh.eeeehhhhh...hhhhh.............ee.............hhh.ee...hhhhhhhhhhhhhh.....eeee...ee..........eeeee.....hhhhhhhhhhhhhh.......eeeeee..............................hhhhh.eee...ee.ee..eeeee........hhhhhhhh....hhhhhhhh......eeee.hhhhh........hhhhhhhhhhhhhhhhhhh...eeee.....hhhhh.......ee.....hhhhhhhhhhh..........hhhhhhhhhhhhhh..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhh....eeeee...........................hhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeee....eeeeeee.....eeeeehhhhhh.....eeee.....eee.....eeeee...eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d0g A   1 AANDNNVEWNGLFHDQGPLFDNAPEPTSTQSVTLKLRTFKGDITSANIKYWDTADNAFHWVPMVWDSNDPTGTFDYWKGTIPASPSIKYYRFQINDGTSTAWYNGNGPSSTEPNADDFYIIPNFKTPDWLKNGVMYQIFPDRFYNGDSSNDVQTGSYTYNGTPTEKKAWGSSVYADPGYDNSLVFFGGDLAGIDQKLGYIKKTLGANILYLNPIFKAPTNHKYDTQDYMAVDPAFGDNSTLQTLINDIHSTANGPKGYLILDGVFNHTGDSHPWFDKYNNFSSQGAYESQSSPWYNYYTFYTWPDSYASFLGFNSLPKLNYGNSGSAVRGVIYNNSNSVAKTYLNPPYSVDGWRLNAAQYVDANGNNGSDVTNHQIWSEFRNAVKGVNSNAAIIGQYWGNANPWTAQGNQWDAATNFDGFTQPVSEWITGKDYQNNSASISTTQFDSWLRGTRANYPTNVQQSMMNFLSNHDITRFATRSGGDLWKTYLALIFQMTYVGTPTIYYGDEYGMQGGADPDNRRSFDWSQATPSNSAVALTQKLITIRNQYPALRTGSFMTLITDDTNKIYSYGRFDNVNRIAVVLNNDSVSHTVNVPVWQLSMPNGSTVTDKITGHSYTVQNGMVTVAVDGHYGAVLAQ 637
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630
   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  (3, 3)

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

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D0G)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEPU1_THEVU | Q60053)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031216    neopullulanase activity    Catalysis of the hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
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.
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 ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ 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 ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:516 - Pro A:517   [ RasMol ]  
    Pro A:346 - Pro A:347   [ RasMol ]  
    Trp A:303 - Pro A:304   [ 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
  2d0g
    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
  NEPU1_THEVU | Q60053
    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
  NEPU1_THEVU | Q60053
    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
        NEPU1_THEVU | Q60053: 1izj 1izk 1ji1 1uh2 1uh3 1uh4 2d0f 2d0h

(-) Related Entries Specified in the PDB File

1ji1 CRYSTAL STRUCTURE ANALYSIS OF THERMOACTINOMYCES VULGARIS R- 47 ALPHA-AMYLASE 1
2d0f THE SAME PROTEIN, D356N MUTANT COMPLEXED WITH P2, A PULLULAN MODEL OLIGOSACCHARIDE
2d0h THE SAME PROTEIN, D356N/E396Q MUTANT COMPLEXED WITH P2, A PULLULAN MODEL OLIGOSACCHARIDE