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(-) Description

Title :  HUMAN PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH MYRICETIN
 
Authors :  L. K. Williams, G. D. Brayer
Date :  23 Aug 12  (Deposition) - 24 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyl Hydrolase, Diabetes, Obesity, Digestion, Glycosidase, Enzyme Inhibition, Flavonol, Drug Design, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. K. Williams, C. Li, S. G. Withers, G. D. Brayer
Order And Disorder: Differential Structural Impacts Of Myricetin And Ethyl Caffeate On Human Amylase, An Antidiabetic Target.
J. Med. Chem. V. 55 10177 2012
PubMed-ID: 23050660  |  Reference-DOI: 10.1021/JM301273U

(-) Compounds

Molecule 1 - PANCREATIC ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Taxid: 4922
    Fragment: UNP RESIDUES 16-511
    Gene: AMY2A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PA, 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  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3MYC1Ligand/Ion3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:140 , ARG A:176 , TRP A:203 , ASP A:206 , ASN A:459 , ASN A:461 , HOH A:820 , HOH A:826 , HOH A:1107 , HOH A:1126BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREARG A:195 , ASN A:298 , ARG A:337BINDING SITE FOR RESIDUE CL A 503
4AC4SOFTWARETRP A:59 , TYR A:62 , GLN A:63 , HIS A:101 , THR A:163 , ASP A:197 , ALA A:198 , GLU A:233 , ASP A:433 , HOH A:1144 , HOH A:1177 , HOH A:1182 , HOH A:1204 , HOH A:1244BINDING SITE FOR RESIDUE MYC A 504

(-) 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  (0, 0)

(no "Cis Peptide Bond" information available for 4GQR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GQR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GQR)

(-) Exons   (0, 0)

(no "Exon" information available for 4GQR)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4gqra1 A:1-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                               d4gqra2 A:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhhh..eeeeee...eeee...........................hhhhh................hhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eee.....hhhhh...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
                 4gqr A   1 xYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GQR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GQR)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  4gqr
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  AMYP_HUMAN | P04746
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  3.2.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYP_HUMAN | P04746: 1b2y 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 3old 3ole 3olg 3oli 4gqq 4w93 4x9y 5e0f 5emy 5kez 5td4

(-) Related Entries Specified in the PDB File

1bsi HUMAN PANCREATIC ALPHA-AMYLASE EXPRESSED IN PICHIA PASTORIS
1cpu HUMAN PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH ACARBOSE
1hny HUMAN PANCREATIC ALPHA-AMYLASE
3ij7 HUMAN PANCREATIC ALPHA-AMYLASE WITH COVALENT GLYCOSYL- ENZYME INTERMEDIATE
3ij8 HUMAN PANCREATIC ALPHA-AMYLASE WITH COVALENT GLYCOSYL- ENZYME INTERMEDIATE
4gqq HUMAN PANCREATIC ALPHA-AMYLASE WITH BOUND ETHYL CAFFEATE