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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SALIVARY ALPHA-AMYLASE DIMER
 
Authors :  S. Z. Fisher, L. Govindasamy, C. K. Tu, D. N. Silverman, H. Rajaniemi, R. Mckenna
Date :  27 Oct 04  (Deposition) - 11 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hsa, Human Salivary Alpha-Amylase, Dimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Z. Fisher, L. Govindasamy, C. K. Tu, D. N. Silverman, H. Rajaniemi, R. Mckenna
Crystal Structure Of Human Salivary Alpha-Amylase Dimer
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A, B
    EC Number: 3.2.1.1
    Fragment: HSA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
    Tissue: SALIVA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:510BINDING SITE FOR RESIDUE CA A 497
2AC2SOFTWAREASN B:100 , ARG B:158 , ASP B:167 , HIS B:201 , HOH B:513BINDING SITE FOR RESIDUE CA B 497
3AC3SOFTWAREARG B:195 , ASN B:298 , ARG B:337BINDING SITE FOR RESIDUE CL B 498
4AC4SOFTWAREARG A:195 , ASN A:298 , ARG A:337BINDING SITE FOR RESIDUE CL A 498

(-) SS Bonds  (10, 10)

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
6B:28 -B:86
7B:70 -B:115
8B:141 -B:160
9B:378 -B:384
10B:450 -B:462

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:53 -Pro A:54
2Val A:129 -Pro A:130
3Asn B:53 -Pro B:54
4Val B:129 -Pro B:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XV8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XV8)

(-) Exons   (10, 20)

Asymmetric/Biological Unit (10, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003700831cENSE00001800716chr1:104198377-104198550174AMY1_HUMAN-00--
1.3ENST000003700833ENSE00001618329chr1:104198907-104199120214AMY1_HUMAN1-56562A:1-41
B:1-41		41
41
1.4bENST000003700834bENSE00002198690chr1:104199466-104199612147AMY1_HUMAN57-105492A:42-90
B:42-90		49
49
1.5ENST000003700835ENSE00001722064chr1:104200416-104200613198AMY1_HUMAN106-171662A:91-156
B:91-156		66
66
1.6bENST000003700836bENSE00002145789chr1:104201062-104201292231AMY1_HUMAN172-248772A:157-233
B:157-233		77
77
1.7ENST000003700837ENSE00001650327chr1:104202032-104202165134AMY1_HUMAN249-293452A:234-278
B:234-278		45
45
1.8ENST000003700838ENSE00001669527chr1:104202982-104203104123AMY1_HUMAN293-334422A:278-319
B:278-319		42
42
1.9ENST000003700839ENSE00001786647chr1:104203199-104203298100AMY1_HUMAN334-367342A:319-352
B:319-352		34
34
1.10aENST0000037008310aENSE00001615366chr1:104205279-104205397119AMY1_HUMAN368-407402A:353-392
B:353-392		40
40
1.11ENST0000037008311ENSE00001680728chr1:104205508-104205633126AMY1_HUMAN407-449432A:392-434
B:392-434		43
43
1.13aENST0000037008313aENSE00001671242chr1:104206953-104207173221AMY1_HUMAN449-511632A:434-496
B:434-496		63
63

(-) 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 AMY1_HUMAN | P04745 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      
           AMY1_HUMAN    16 QYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 511
               SCOP domains d1xv8a2 A:1-408 automated matches                                                                                                                                                                                                                                                                                                                                                                                       d1xv8a1 A:409-496 automated matches                                                      SCOP domains
               CATH domains -1xv8A01 A:2-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                      1xv8A02 A:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eee.................hhhhh...........hhhhhhhhhhhhhh...eeeeee...eeee...........................hhhhh................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...............eeee..........hhhhhh...eeehhhhhhhhhhhhh.....hhhhhh..hhhhh..hhh.eee.....hhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee.......ee..ee..............................hhhhhhhhhhhhhhhhhh....eeeee.......eeee...eeeee......eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-41 UniProt: 1-56      Exon 1.4b  PDB: A:42-90 UniProt: 57-105          Exon 1.5  PDB: A:91-156 UniProt: 106-171                          Exon 1.6b  PDB: A:157-233 UniProt: 172-248                                   Exon 1.7  PDB: A:234-278 UniProt: 249-293    ----------------------------------------Exon 1.9  PDB: A:319-352          Exon 1.10a  PDB: A:353-392              -----------------------------------------Exon 1.13a  PDB: A:434-496 UniProt: 449-511                     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:278-319 UniProt: 293-334 ------------------------------------------------------------------------Exon 1.11  PDB: A:392-434 UniProt: 407-449 -------------------------------------------------------------- Transcript 1 (2)
                 1xv8 A   1 xYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 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      
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                            1-PCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:496
 aligned with AMY1_HUMAN | P04745 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      
           AMY1_HUMAN    16 QYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 511
               SCOP domains d1xv8b2 B:1-408 automated matches                                                                                                                                                                                                                                                                                                                                                                                       d1xv8b1 B:409-496 automated matches                                                      SCOP domains
               CATH domains -1xv8B01 B:2-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                      1xv8B02 B:404-496 Golgi alpha-mannosidase II                                                  CATH domains
           Pfam domains (1) --------------------Alpha-amylase-1xv8B03 B:21-336                                                                                                                                                                                                                                                                                              ---------------------------------------------------------------------Alpha-amylase_C-1xv8B01 B:406-495                                                         - Pfam domains (1)
           Pfam domains (2) --------------------Alpha-amylase-1xv8B04 B:21-336                                                                                                                                                                                                                                                                                              ---------------------------------------------------------------------Alpha-amylase_C-1xv8B02 B:406-495                                                         - Pfam domains (2)
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eee.................hhhhh...........hhhhhhhhhhhhhh...eeeeee...eeee...........................hhhhh................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...............eeee..........hhhhhh...eeehhhhhhhhhhhhh.....hhhhhh..hhhhh..hhh.eee.....hhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee.......ee..ee..............................hhhhhhhhhhhhhhhhhh....eeeee.......eeee...eeeee......eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:1-41 UniProt: 1-56      Exon 1.4b  PDB: B:42-90 UniProt: 57-105          Exon 1.5  PDB: B:91-156 UniProt: 106-171                          Exon 1.6b  PDB: B:157-233 UniProt: 172-248                                   Exon 1.7  PDB: B:234-278 UniProt: 249-293    ----------------------------------------Exon 1.9  PDB: B:319-352          Exon 1.10a  PDB: B:353-392              -----------------------------------------Exon 1.13a  PDB: B:434-496 UniProt: 449-511                     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:278-319 UniProt: 293-334 ------------------------------------------------------------------------Exon 1.11  PDB: B:392-434 UniProt: 407-449 -------------------------------------------------------------- Transcript 1 (2)
                 1xv8 B   1 xYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 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      
                            1-PCA
   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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AMY1_HUMAN | P04745)
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: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: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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    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: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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  1xv8
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMY1_HUMAN | P04745: 1c8q 1jxj 1jxk 1mfu 1mfv 1nm9 1q4n 1smd 1z32 3blk 3blp 3dhp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XV8)