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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF THE POTATO INHIBITOR COMPLEX OF CARBOXYPEPTIDASE A AT 2.5 ANGSTROMS RESOLUTION
 
Authors :  W. N. Lipscomb, D. C. Rees
Date :  24 Mar 82  (Deposition) - 29 Jul 82  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,I,J
Biol. Unit 1:  A,I  (1x)
Biol. Unit 2:  B,J  (1x)
Keywords :  Hydrolase (C-Terminal Peptidase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. C. Rees, W. N. Lipscomb
Refined Crystal Structure Of The Potato Inhibitor Complex O Carboxypeptidase A At 2. 5 A Resolution.
J. Mol. Biol. V. 160 475 1982
PubMed-ID: 7154070  |  Reference-DOI: 10.1016/0022-2836(82)90309-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE A
    ChainsA, B
    EC Number3.4.17.1
    EngineeredYES
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
 
Molecule 2 - METALLOCARBOXYPEPTIDASE INHIBITOR
    ChainsI, J
    EngineeredYES
    Organism CommonPOTATO
    Organism ScientificSOLANUM TUBEROSUM
    Organism Taxid4113

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABIJ
Biological Unit 1 (1x)A I 
Biological Unit 2 (1x) B J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GLY1Mod. Amino AcidGLYCINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GLY1Mod. Amino AcidGLYCINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , VAL I:38BINDING SITE FOR RESIDUE ZN I 308
2AC2SOFTWAREHIS B:69 , GLU B:72 , HIS B:196 , VAL J:38BINDING SITE FOR RESIDUE ZN J 309
3AC3SOFTWAREHIS A:69 , ASN A:144 , ARG A:145 , ILE A:247 , TYR A:248 , GLU A:270 , VAL I:38BINDING SITE FOR RESIDUE GLY A 308
4AC4SOFTWAREHIS B:69 , ASN B:144 , ARG B:145 , ILE B:247 , TYR B:248 , GLU B:270 , VAL J:38BINDING SITE FOR RESIDUE GLY B 308

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:138 -A:161
2B:138 -B:161
3I:8 -I:24
4I:12 -I:27
5I:18 -I:34
6J:8 -J:24
7J:12 -J:27
8J:18 -J:34

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:197 -Tyr A:198
2Pro A:205 -Tyr A:206
3Ser B:197 -Tyr B:198
4Pro B:205 -Tyr B:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CBPA1_BOVIN_001 *I289VCBPA1_BOVIN  ---  ---A/BI179V
2UniProtVAR_CBPA1_BOVIN_002 *E338ACBPA1_BOVIN  ---  ---A/BA228A
3UniProtVAR_CBPA1_BOVIN_003 *L415VCBPA1_BOVIN  ---  ---A/BV305V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CBPA1_BOVIN_001 *I289VCBPA1_BOVIN  ---  ---AI179V
2UniProtVAR_CBPA1_BOVIN_002 *E338ACBPA1_BOVIN  ---  ---AA228A
3UniProtVAR_CBPA1_BOVIN_003 *L415VCBPA1_BOVIN  ---  ---AV305V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CBPA1_BOVIN_001 *I289VCBPA1_BOVIN  ---  ---BI179V
2UniProtVAR_CBPA1_BOVIN_002 *E338ACBPA1_BOVIN  ---  ---BA228A
3UniProtVAR_CBPA1_BOVIN_003 *L415VCBPA1_BOVIN  ---  ---BV305V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPA1_BOVIN170-192
 
  2A:60-82
B:60-82
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPA1_BOVIN306-316
 
  2A:196-206
B:196-206
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPA1_BOVIN170-192
 
  1A:60-82
-
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPA1_BOVIN306-316
 
  1A:196-206
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPA1_BOVIN170-192
 
  1-
B:60-82
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPA1_BOVIN306-316
 
  1-
B:196-206

(-) Exons   (0, 0)

(no "Exon" information available for 4CPA)

(-) Sequences/Alignments

Asymmetric 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:308
 aligned with CBPA1_BOVIN | P00730 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:309
                                   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         
          CBPA1_BOVIN   111 ARSTNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTLNNLY 419
               SCOP domains d4cpaa_ A: Carboxypeptidase A                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 4cpaA00 A:1-307 Zn peptidases                                                                                                                                                                                                                                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...eeeee............eeeee......eeeeeee.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhheeeeee..hhhhhhhhhhh..................................................hhhhhhhhhhhhhhh..eeeeeee...eeeee..........hhhhhhhhhhhhhhhhh.......eee............hhhhhhhhh..eeeeeee.............hhhhhhhhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------A----------------------------------------------------------------------------V---- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cpa A   1 ARSTNTFNYATYHTLDEIYDFMDLLVAQHPELVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTENYGQNPSFTAILDSMDIFLEIVTNPNGFAFTHSENRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKNHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVAALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTVNN-G 308
                                    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      | |
                                                                                                                                                                                                                                                                                                                                            307 |
                                                                                                                                                                                                                                                                                                                                              308

Chain B from PDB  Type:PROTEIN  Length:308
 aligned with CBPA1_BOVIN | P00730 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:308
                                   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        
          CBPA1_BOVIN   111 ARSTNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTLNNL 418
               SCOP domains d4cpab_ B: Carboxypeptidase A                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 4cpaB00 B:1-307 Zn peptidases                                                                                                                                                                                                                                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...eeeee............eeeee......eeeeeee.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhheeeeee..hhhhhhhhhhh..................................................hhhhhhhhhhhhhhh..eeeeeee...eeeee..........hhhhhhhhhhhhhhhhh.......eee............hhhhhhhhh..eeeeeee.............hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------A----------------------------------------------------------------------------V--- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cpa B   1 ARSTNTFNYATYHTLDEIYDFMDLLVAQHPELVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTENYGQNPSFTAILDSMDIFLEIVTNPNGFAFTHSENRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKNHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVAALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTVNNG 308
                                    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        

Chain I from PDB  Type:PROTEIN  Length:37
 aligned with MCPI_SOLTU | P01075 from UniProtKB/Swiss-Prot  Length:39

    Alignment length:37
                                    11        21        31       
           MCPI_SOLTU     2 QHADPICNKPCKTHDDCSGAWFCQACWNSARTCGPYV  38
               SCOP domains d4cpai_ I:                            SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 4cpa I   2 ZHADPICNKPCKTHDDCSGAWFCQACWNSARTCGPYV  38
                                    11        21        31       

Chain J from PDB  Type:PROTEIN  Length:37
 aligned with MCPI_SOLTU | P01075 from UniProtKB/Swiss-Prot  Length:39

    Alignment length:37
                                    11        21        31       
           MCPI_SOLTU     2 QHADPICNKPCKTHDDCSGAWFCQACWNSARTCGPYV  38
               SCOP domains d4cpaj_ J:                            SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 4cpa J   2 ZHADPICNKPCKTHDDCSGAWFCQACWNSARTCGPYV  38
                                    11        21        31       

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CBPA1_BOVIN | P00730)
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.

Chain I,J   (MCPI_SOLTU | P01075)
molecular function
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBPA1_BOVIN | P007301arl 1arm 1bav 1cbx 1cps 1cpx 1ee3 1ell 1elm 1f57 1hdq 1hdu 1hee 1iy7 1m4l 1pyt 1yme 1zlh 2abz 2ctb 2ctc 2rfh 3cpa 3fvl 3fx6 3i1u 3kgq 5cpa 6cpa 7cpa 8cpa
        MCPI_SOLTU | P010751h20

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4CPA)