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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-AMYLASE IN COMPLEX WITH ACARVIOSTATIN I03
 
Authors :  X. Qin, L. Ren
Date :  26 Aug 10  (Deposition) - 13 Apr 11  (Release) - 27 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosylation, Hydrolase-Hydrolase Inhibitor Complex, Acarviostatin I03 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Qin, L. Ren, X. Yang, F. Bai, L. Wang, P. Geng, G. Bai, Y. Shen
Structures Of Human Pancreatic Alpha-Amylase In Complex Wit Acarviostatins: Implications For Drug Design Against Type I Diabetes
J. Struct. Biol. V. 174 196 2011
PubMed-ID: 21111049  |  Reference-DOI: 10.1016/J.JSB.2010.11.020

(-) Compounds

Molecule 1 - PANCREATIC ALPHA-AMYLASE
    ChainsA
    EC Number3.2.1.1
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonYEAST
    Expression System Taxid4932
    GeneAMY2A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPA, 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 18)

Asymmetric/Biological Unit (10, 18)
No.NameCountTypeFull Name
1ACI1Ligand/Ion6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA1Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5G6D1Ligand/Ion6-DEOXY-ALPHA-D-GLUCOSE
6GLC9Ligand/IonALPHA-D-GLUCOSE
7MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
8NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
9PCA1Ligand/IonPYROGLUTAMIC ACID
10SO41Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:518 , HOH A:531 , HOH A:815BINDING SITE FOR RESIDUE CA A 497
02AC2SOFTWAREARG A:195 , ASN A:298 , ARG A:337BINDING SITE FOR RESIDUE CL A 498
03AC3SOFTWAREASN A:53 , TRP A:59BINDING SITE FOR RESIDUE SO4 A 499
04AC4SOFTWAREGLU A:171 , ARG A:176 , ASP A:206 , ASN A:459 , GLY A:460 , ASN A:461 , HOH A:620 , HOH A:651BINDING SITE FOR RESIDUE NAG A 500
05AC5SOFTWAREGLC A:508 , HOH A:569BINDING SITE FOR RESIDUE GLC A 507
06AC6SOFTWARETYR A:131 , SER A:132 , TRP A:134 , ASP A:135 , TYR A:174 , GLC A:507 , GLC A:509 , HOH A:564BINDING SITE FOR RESIDUE GLC A 508
07AC7SOFTWAREGLN A:8 , TRP A:134 , ASP A:135 , LYS A:172 , TYR A:174 , GLC A:508 , HOH A:613BINDING SITE FOR RESIDUE GLC A 509
08AC8SOFTWARETYR A:2 , PRO A:228 , PHE A:229 , ILE A:230 , ASN A:250 , HOH A:706BINDING SITE FOR RESIDUE PCA A 510
09AC9SOFTWARETHR A:376 , ARG A:387 , TRP A:388 , ARG A:389 , GLN A:390 , GLU A:484 , GLC A:512 , HOH A:621BINDING SITE FOR RESIDUE GLC A 511
10BC1SOFTWAREALA A:318 , LYS A:322 , THR A:377 , TRP A:388 , GLN A:390 , GLC A:511 , BGC A:513 , HOH A:743 , HOH A:782BINDING SITE FOR RESIDUE GLC A 512
11BC2SOFTWAREARG A:343 , GLC A:512 , HOH A:766BINDING SITE FOR RESIDUE BGC A 513
12BC3SOFTWAREHIS A:305 , GLY A:306 , ASP A:433 , ASN A:481 , SER A:482 , GLC A:502BINDING SITE FOR RESIDUE MPD A 514
13BC4SOFTWARETRP A:58 , TRP A:59 , TYR A:62 , GLN A:63 , HIS A:101 , GLY A:104 , TYR A:151 , THR A:163 , ARG A:195 , ASP A:197 , ALA A:198 , LYS A:200 , HIS A:201 , GLU A:233 , ILE A:235 , LEU A:237 , GLU A:240 , HIS A:299 , ASP A:300 , HIS A:305 , GLY A:306 , ASP A:433 , TRP A:434 , MPD A:514 , HOH A:666 , HOH A:685 , HOH A:710 , HOH A:727 , HOH A:825BINDING SITE FOR LINKED RESIDUES A 501 to 506

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:86
2A:70 -A:115
3A:141 -A:160
4A:378 -A:384
5A:450 -A:462

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:53 -Pro A:54
2Val A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OLD)

(-) 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:495
 aligned with AMYP_HUMAN | P04746 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:495
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506     
           AMYP_HUMAN    17 YSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 511
               SCOP domains d3olda1 A:2-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                              d3olda2 A:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------Alpha-amylase-3oldA02 A:21-336                                                                                                                                                                                                                                                                                              ---------------------------------------------------------------------Alpha-amylase_C-3oldA01 A:406-495                                                         - Pfam domains
         Sec.struct. author ..........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhhh..eeeeee...eeee...............hhhhh.......hhhhh................hhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eee.....hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeee.......ee..ee........ee..ee................hhhhhhhhhhhhhhhhhh....eeeeee....eeeeee...eeeeee.....eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3old A   2 YSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 496
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491     

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: GHD (106)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYP_HUMAN | P04746)
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.
    GO:0044245    polysaccharide digestion    The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested polysaccharides into components that may be easily absorbed and directed into metabolism.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYP_HUMAN | P047461b2y 1bsi 1cpu 1hny 1kb3 1kbb 1kbk 1kgu 1kgw 1kgx 1u2y 1u30 1u33 1xcw 1xcx 1xd0 1xd1 1xgz 1xh0 1xh1 1xh2 2cpu 2qmk 2qv4 3bai 3baj 3bak 3baw 3bax 3bay 3cpu 3ij7 3ij8 3ij9 3ole 3olg 3oli 4gqq 4gqr 4w93 4x9y 5e0f 5emy 5kez 5td4

(-) Related Entries Specified in the PDB File

3ole 3olg