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(-) Description

Title :  PIG PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THE PROTEINACEOUS INHIBITOR TENDAMISTAT
 
Authors :  M. Machius, G. Wiegand, O. Epp, R. Huber
Date :  16 Sep 98  (Deposition) - 23 Sep 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  P,T
Keywords :  Glycosyltransferase, Alpha-1, 4-Glucan-4-Glucanohydrolase, Alpha-Amylase, Proteinaceous Alpha-Amylase Inhibitor, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Wiegand, O. Epp, R. Huber
The Crystal Structure Of Porcine Pancreatic Alpha-Amylase In Complex With The Microbial Inhibitor Tendamistat.
J. Mol. Biol. V. 247 99 1995
PubMed-ID: 7897663  |  Reference-DOI: 10.1006/JMBI.1994.0125
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ALPHA-AMYLASE)
    Chains: P
    EC Number: 3.2.1.1
    Organ: PANCREAS
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: 1,4-GLUCAN-4-GLUCANOHYDROLASE, GLYCOSYLTRANSFERASE
 
Molecule 2 - PROTEIN (TENDAMISTAT)
    Chains: T
    Organism Scientific: STREPTOMYCES TENDAE
    Organism Taxid: 1932
    Strain: 4158

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : PT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN P:100 , ARG P:158 , ASP P:167 , HIS P:201 , HOH P:1152BINDING SITE FOR RESIDUE CA P 2001
2AC2SOFTWAREARG P:195 , ARG P:337BINDING SITE FOR RESIDUE CL P 2002
3ASAUTHORASP P:197 , GLU P:233 , ASP P:300CATALYTICALLY ACTIVE RESIDUES.
4CAAUTHORASN P:100 , ARG P:158 , ASP P:167 , HIS P:201CALCIUM BINDING SITE.
5CLAUTHORARG P:195 , ASN P:298 , ARG P:337CHLORIDE BINDING SITE.

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1P:28 -P:86
2P:70 -P:115
3P:141 -P:160
4P:378 -P:384
5P:450 -P:462
6T:811 -T:827
7T:845 -T:873

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val P:129 -Pro P:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BVN)

(-) 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 P from PDB  Type:PROTEIN  Length:496
 aligned with AMYP_PIG | P00690 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:496
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505      
             AMYP_PIG    16 QYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGNREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIQSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKVAVGFMLAHPYGFTRVMSSYRWARNFVNGQDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWRQIRNMVWFRNVVDGQPFANWWANGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 511
               SCOP domains d1bvnp2 P:1-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                               d1bvnp1 P:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains 1bvnP01 P:1-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                       1bvnP02 P:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....hhhhhhhhhh........eee................hhh...............hhhhhhhhhhhhhh..eeeeee.......................hhh.........hhh..................hhhhhh.............hhhhhhhhhhhhhhhhh...eeee..hhh..hhhhhhhhhh...............eeee...........hhhh........hhhhhhhhhhh.......hhhhhh..hhh....hhh.........hhh...........hhhhhhhhhhhhhhhh.....eeeee............................................hhh.hhhhhhhhhhhh...............eeeeee...eeeeee.....eeeeee.....eeee...............eeee....eeeeee.......eeeeehhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bvn P   1 QYAPQTQSGRTDIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENVVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGSREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRLDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAISSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGSSILTFWDARLYKVAVGFMLAHPYGFTRVMSSYRWARNFVNGEDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWREIRNMVWFRNVVDGQPFANWWDNGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCNVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAQDPFIAIHAESKL 496
                                    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      


Chain T from PDB  Type:PROTEIN  Length:71
 aligned with IAA_STRTE | P01092 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:71
                                    43        53        63        73        83        93       103 
            IAA_STRTE    34 VSEPAPSCVTLYQSWRYSQADNGCAQTVTVKVVYEDDTEGLCYAVAPGQITTVGDGYIGSHGHARYLARCL 104
               SCOP domains d1bvnt_ T: alpha-Amylase inhibitor tendamistat                          SCOP domains
               CATH domains 1bvnT00 T:804-874 Alpha-Amylase inhibitor                               CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...eeeeee.....eeeeeee........eee....eeeeee........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 1bvn T 804 VSEPAPSCVTLYQSWRYSQADNGCAETVTVKVVYEDDTEGLCYAVAPGQITTVGDGYIGSHGHARYLARCL 874
                                   813       823       833       843       853       863       873
   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 1BVN)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (AMYP_PIG | P00690)
molecular function
    GO:0004556    alpha-amylase activity    Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
    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:0031404    chloride ion binding    Interacting selectively and non-covalently with chloride ions (Cl-).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Chain T   (IAA_STRTE | P01092)
molecular function
    GO:0015066    alpha-amylase inhibitor activity    Stops, prevents or reduces the activity of alpha-amylase.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.

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  Cis Peptide Bonds
    Val P:129 - Pro P:130   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYP_PIG | P00690: 1dhk 1hx0 1jfh 1kxq 1kxt 1kxv 1ose 1pif 1pig 1ppi 1ua3 1vah 1wo2 3l2l 3l2m 4x0n
        IAA_STRTE | P01092: 1hoe 1ok0 2ait 3ait 4ait

(-) Related Entries Specified in the PDB File

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