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(-) Description

Title :  CARBOXYPEPTIDASE B IN COMPLEX WITH DD9
 
Authors :  N. Yoshimoto, T. Itoh, Y. Inaba, K. Yamamoto
Date :  24 May 13  (Deposition) - 02 Oct 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Selen, Organoselenium, Selenium, Selenol, Cpb Inhibitor, Second Zinc, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Yoshimoto, T. Itoh, Y. Inaba, H. Ishii, K. Yamamoto
Structural Basis For Inhibition Of Carboxypeptidase B By Selenium-Containing Inhibitor: Selenium Coordinates To Zinc In Enzyme
J. Med. Chem. 2013
PubMed-ID: 24010887  |  Reference-DOI: 10.1021/JM400816V

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE B
    Chains: A
    EC Number: 3.4.17.2
    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  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2DDK1Ligand/Ion(2R)-7-AMINO-2-(SELANYLMETHYL)HEPTANOIC ACID
3ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:85 , ASP A:159 , ASP A:162 , GLU A:291 , HOH A:823BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , DDK A:403BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREHIS A:69 , GLU A:72 , ARG A:127 , ASN A:144 , ARG A:145 , HIS A:196 , SER A:207 , ILE A:247 , TYR A:248 , ASP A:255 , GLU A:270 , ZN A:402 , ZN A:404 , HOH A:575BINDING SITE FOR RESIDUE DDK A 403
4AC4SOFTWARESER A:197 , TYR A:198 , GLU A:270 , DDK A:403 , CAC A:405BINDING SITE FOR RESIDUE ZN A 404
5AC5SOFTWARESER A:197 , TYR A:198 , ILE A:247 , TYR A:248 , GLU A:270 , PHE A:279 , ZN A:404 , HOH A:824BINDING SITE FOR RESIDUE CAC A 405

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:79
2A:138 -A:161
3A:152 -A:166

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:197 -Tyr A:198
2Pro A:205 -Tyr A:206
3Arg A:272 -Asp A:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WC5)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPB1_PIG167-189  1A:60-82
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPB1_PIG304-314  1A:196-206

(-) Exons   (0, 0)

(no "Exon" information available for 3WC5)

(-) 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:304
 aligned with CBPB1_PIG | P09955 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:304
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412    
           CBPB1_PIG    113 GHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  416
               SCOP domains d3wc5a_ A: Carboxypeptidase B                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeee......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3wc5 A    6 GHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185  |    194       204       214       224       234       244       254       264       274       284       294       304    
                                                                                                                                                                                                               187A
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WC5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WC5)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPB1_PIG | P09955)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004181    metallocarboxypeptidase activity    Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

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  3.4.17.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        CBPB1_PIG | P09955: 1nsa 1pba 1z5r 1zg7 1zg8 1zg9 2jew 2piy 2piz 2pj0 2pj1 2pj2 2pj3 2pj4 2pj5 2pj6 2pj7 2pj8 2pj9 2pja 2pjb 2pjc 3glj 3wab 3wc6 3wc7 4uia 4uib 4z65 5j1q 5jc6 5lrg 5lrj 5lrk 5lyd 5lyf 5lyi 5lyl

(-) Related Entries Specified in the PDB File

3wab 3wc6 3wc7