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 :  CRYSTAL STRUCTURE OF THE PIG PANCREATIC A-AMYLASE COMPLEXED WITH MALTO-OLIGOSACCHARIDES
 
Authors :  F. Payan, M. Qian
Date :  27 Feb 03  (Deposition) - 14 Oct 03  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-Barrels, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Payan, M. Qian
Crystal Structure Of The Pig Pancreatic Alpha-Amylase Complexed With Malto-Oligosaccharides
J. Protein Chem. V. 22 275 2003
PubMed-ID: 12962327  |  Reference-DOI: 10.1023/A:1025072520607
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE, PANCREATIC
    Chains: A
    EC Number: 3.2.1.1
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA1Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4EDO6Ligand/Ion1,2-ETHANEDIOL
5MAL1Ligand/IonMALTOSE
6MLR2Ligand/IonMALTOTRIOSE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:140 , TRP A:203 , GLY A:205 , ASP A:206 , CL A:499 , HOH A:577 , HOH A:1027 , HOH A:1082 , HOH A:1197BINDING SITE FOR RESIDUE BGC A 1997
02AC2SOFTWAREALA A:318 , LYS A:322 , THR A:376 , THR A:377 , ARG A:387 , TRP A:388 , ARG A:389 , GLU A:390 , HOH A:661 , HOH A:750 , HOH A:967 , HOH A:1035 , HOH A:1080 , HOH A:1162 , HOH A:1198 , HOH A:1199BINDING SITE FOR RESIDUE MAL A 1998
03AC3SOFTWAREARG A:195 , ASN A:298 , ARG A:337BINDING SITE FOR RESIDUE CL A 498
04AC4SOFTWARETRP A:203 , PRO A:204 , GLY A:205 , BGC A:1997BINDING SITE FOR RESIDUE CL A 499
05AC5SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:520 , HOH A:527 , HOH A:539BINDING SITE FOR RESIDUE CA A 500
06AC6SOFTWARETRP A:58 , TRP A:59 , TYR A:62 , GLN A:63 , HIS A:101 , GLY A:104 , VAL A:163 , ARG A:195 , ASP A:197 , GLU A:233 , HIS A:299 , ASP A:300 , HOH A:812 , HOH A:1092 , HOH A:1187 , HOH A:1190BINDING SITE FOR RESIDUE MLR A 1990
07AC7SOFTWARETHR A:52 , ASN A:53 , ALA A:108 , LYS A:261 , GLU A:272 , TYR A:276 , ASN A:279 , GLY A:283 , TRP A:284 , HOH A:1134 , HOH A:1146 , HOH A:1191 , HOH A:1193 , HOH A:1195 , HOH A:1282BINDING SITE FOR RESIDUE MLR A 1994
08AC8SOFTWARESER A:132 , ASP A:135 , TYR A:174 , EDO A:2001BINDING SITE FOR RESIDUE EDO A 2000
09AC9SOFTWAREASP A:135 , LYS A:172 , TYR A:174 , EDO A:2000BINDING SITE FOR RESIDUE EDO A 2001
10BC1SOFTWARETHR A:114 , CYS A:115 , GLY A:116 , HOH A:1025 , HOH A:1266BINDING SITE FOR RESIDUE EDO A 2002
11BC2SOFTWARELYS A:213 , LEU A:214 , HIS A:215 , LYS A:466 , VAL A:467 , TYR A:468 , HOH A:841 , HOH A:1307 , EDO A:2004BINDING SITE FOR RESIDUE EDO A 2003
12BC3SOFTWARELYS A:466 , VAL A:467 , GLN A:476 , PHE A:477 , SER A:478 , HOH A:1307 , EDO A:2003BINDING SITE FOR RESIDUE EDO A 2004
13BC4SOFTWAREARG A:30 , THR A:376 , ARG A:387 , HOH A:1256 , HOH A:1287BINDING SITE FOR RESIDUE EDO A 2005

(-) 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 1UA3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UA3)

(-) Exons   (0, 0)

(no "Exon" information available for 1UA3)

(-) 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: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 d1ua3a2 A:1-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                               d1ua3a1 A:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains 1ua3A01 A:1-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                       1ua3A02 A:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains ---------------------Alpha-amylase-1ua3A02 A:22-336                                                                                                                                                                                                                                                                                             ------------------------------------------------------------------------Alpha-amylase_C-1ua3A01 A:409-481                                        --------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhhh..eeeeee...eeee...............hhhhh.......hhhhh................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eee.hhhhhhhhhhhh.....hhhhhhhhhhhhh..hhh.eee.....hhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee.......ee..ee........ee..ee................hhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee...eeeeee.....eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ua3 A   1 QYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGNREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIKSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGSSILTFWDARLYKIAVGFMLAHPYGFTRVMSSYRWARNFVNGEDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWREIRNMVWFRNVVDGQPFANWWDNGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 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
   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  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (13, 13)

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

 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 ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLR  [ 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 ]
 
  Cis Peptide Bonds
    Asn A:53 - Pro A:54   [ RasMol ]  
    Val A:129 - Pro A:130   [ 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
  1ua3
    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
  AMYP_PIG | P00690
    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
  AMYP_PIG | P00690
    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
        AMYP_PIG | P00690: 1bvn 1dhk 1hx0 1jfh 1kxq 1kxt 1kxv 1ose 1pif 1pig 1ppi 1vah 1wo2 3l2l 3l2m 4x0n

(-) Related Entries Specified in the PDB File

1jfh THE SAME PROTEIN COMPLEXED WITH A SUBSTRATE ANALOGUE