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(-) Description

Title :  STRUCTURE OF HUMAN DPP3 IN COMPLEX WITH MET-ENKEPHALIN
 
Authors :  P. Kumar, V. Reithofer, M. Reisinger, T. Pavkov-Keller, S. Wallner, P. Macheroux, K. Gruber
Date :  01 Oct 15  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex, Opioid-Peptide, Zinc-Hydrolase, Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Kumar, V. Reithofer, M. Reisinger, S. Wallner, T. Pavkov-Keller, P. Macheroux, K. Gruber
Substrate Complexes Of Human Dipeptidyl Peptidase Iii Revea The Mechanism Of Enzyme Inhibition.
Sci Rep V. 6 23787 2016
PubMed-ID: 27025154  |  Reference-DOI: 10.1038/SREP23787

(-) Compounds

Molecule 1 - DIPEPTIDYL PEPTIDASE 3
    ChainsA
    EC Number3.4.14.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System CommonHUMAN
    Expression System PlasmidPET28MHL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDPP3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDIPEPTIDYL AMINOPEPTIDASE III,DIPEPTIDYL ARYLAMIDASE III, DIPEPTIDYL PEPTIDASE III,DPP III,ENKEPHALINASE B
 
Molecule 2 - MET-ENKEPHALIN
    ChainsB
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2MG2Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:450 , HIS A:455 , GLU A:508 , HOH A:1329 , GLY B:2binding site for residue ZN A 801
2AC2SOFTWARESER A:101 , ASN A:102 , SER A:108 , SER A:384 , GLY A:385 , HOH A:1278binding site for residue MG A 802
3AC3SOFTWAREGLY A:162 , GLY A:164 , GLY A:167 , HOH A:1028 , HOH A:1156 , HOH A:1239binding site for residue MG A 803
4AC4SOFTWARESER A:317 , GLY A:323 , ASP A:496 , SER A:504 , HOH A:1009binding site for residue K A 804

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:207 -A:207

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:392 -Pro A:393
2Pro A:651 -Pro A:652

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E33)

(-) Exons   (0, 0)

(no "Exon" information available for 5E33)

(-) 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:725
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.................hhhhhhhhhhhhhhh......eeeeeee.....eeeeeeee............hhhhh.eeee..eeeeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..........eeeeeeeeehhhhhhhhhhhh.hhhhhhhhh..hhhhh.......eeeeeeeeeee......eeee..hhhhhhhh..eeeeehhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh........................................hhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhh...ee....ee.hhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee.hhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhh.....eee..eeeee..eeeee....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e33 A   2 ADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQREKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPETGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIYVNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPDARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRDTVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLATADARFW 726
                                    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       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721     

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .ee.. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5e33 B   1 YGGFM   5

   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 5E33)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E33)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E33)

(-) Gene Ontology  (54, 56)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ile A:392 - Pro A:393   [ RasMol ]  
    Pro A:651 - Pro A:652   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPP3_HUMAN | Q9NY333fvy 3t6b 3t6j 5e2q 5e3a 5e3c 5egy 5ehh
        PENK_HUMAN | P012101plw 1plx 2lwc 5e3a

(-) Related Entries Specified in the PDB File

3fvy CONTAINS THE SAME STRUCTURE IN ITS UNBOUND FORM
3t6b CONTAINS THE SAME PROTEIN IN ITS BOUND FORM