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(-) Description

Title :  SELECTIVE AND POTENT INHIBITION OF THE GLYCOSIDASE HUMAN AMYLASE BY THE SHORT AND EXTREMELY COMPACT PEPTIDE PIHA FROM MRNA DISPLAY
 
Authors :  S. Caner, G. D. Brayer
Date :  10 Jun 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amylase, Diabetes, Obesity, Glucosyl Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Jongkees, S. Caner, C. Tysoe, G. D. Brayer, S. G. Withers, H. Suga
Rapid Discovery Of Potent And Selective Glycosidase-Inhibiting De Novo Peptides.
Cell Chem Biol V. 24 381 2017
PubMed-ID: 28262556  |  Reference-DOI: 10.1016/J.CHEMBIOL.2017.02.001

(-) Compounds

Molecule 1 - PANCREATIC ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: KOMAGATAELLA 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
 
Molecule 2 - ACE-DTY-PRO-TYR-SER-CYS-TRP-VAL-ARG-HIS-NH2
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA1Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4DTY1Mod. Amino AcidD-TYROSINE
5NH21Mod. Amino AcidAMINO GROUP
6PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:195 , ASN A:298 , ARG A:337binding site for residue CL A 501
2AC2SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:687 , HOH A:720 , HOH A:781binding site for residue CA A 502

(-) 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 5KEZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KEZ)

(-) Exons   (0, 0)

(no "Exon" information available for 5KEZ)

(-) 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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...eee.hhhhhhhhhhhhh....hhhhhhhhhhhhh..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
                 5kez 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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5kez B   0 xxPYSCWVRHx  10
                            ||       9|
                            0-ACE    10-NH2
                             1-DTY
   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  (0, 0)

(no "SCOP Domain" information available for 5KEZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KEZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KEZ)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4gqr 4w93 4x9y 5e0f 5emy 5td4

(-) Related Entries Specified in the PDB File

1cpu 1CPU CONTAINS THE SAME PROTEIN COMPLEXED WITH ACARBOSE
4w93 4W93 CONTAINS THE SAME PROTEIN COMPLEXED WITH MONTBRETIN A
4x9y 4X9Y CONTAINS THE SAME PROTEIN WITHOUT INHIBITOR