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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TICK CARBOXYPEPTIDASE INHIBITOR IN COMPLEX WITH BOVINE CARBOXYPEPTIDASE A
 
Authors :  J. L. Arolas, G. M. Popowicz, J. Lorenzo, C. P. Sommerhoff, R. Huber, F. X. Aviles, T. A. Holak
Date :  06 May 05  (Deposition) - 05 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor-Metallocarboxypeptidase Complex, Beta-Defensin Fold (Tci), Eight-Stranded Twisted Beta-Sheet Surrounded By Eight Alpha-Helices (Cpa), Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. L. Arolas, G. M. Popowicz, J. Lorenzo, C. P. Sommerhoff, R. Huber, F. X. Aviles, T. A. Holak
The Three-Dimensional Structures Of Tick Carboxypeptidase Inhibitor In Complex With A/B Carboxypeptidases Reveal A Novel Double-Headed Binding Mode
J. Mol. Biol. V. 350 489 2005
PubMed-ID: 15961103  |  Reference-DOI: 10.1016/J.JMB.2005.05.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE A1
    ChainsA
    EC Number3.4.17.1
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9
    Expression System StrainKM71
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymCARBOXYPEPTIDASE A, CPA, METALLOCARBOXYPEPTIDASE
 
Molecule 2 - CARBOXYPEPTIDASE INHIBITOR
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPBAT4
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificRHIPICEPHALUS BURSA
    Organism Taxid67831
    SynonymINHIBITOR OF A/B METALLOCARBOXYPEPTIDASES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1ZN5Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , LEU B:74BINDING SITE FOR RESIDUE ZN A 555
2AC2SOFTWAREHIS A:120 , ASN B:1 , HOH B:79 , HOH B:155BINDING SITE FOR RESIDUE ZN A 666
3AC3SOFTWAREASP A:16 , HOH A:1117 , HOH A:1216BINDING SITE FOR RESIDUE ZN A 777
4AC4SOFTWAREHIS A:29 , HOH A:1168 , HOH A:1197 , HOH A:1246 , HOH A:1272 , HOH A:1277BINDING SITE FOR RESIDUE ZN A 888
5AC5SOFTWAREHIS A:303 , HOH A:1257 , HOH A:1271BINDING SITE FOR RESIDUE ZN A 999

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:138 -A:161
2B:3 -B:31
3B:10 -B:27
4B:16 -B:32
5B:40 -B:70
6B:47 -B:64
7B:54 -B:71

(-) 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  (3, 3)

Asymmetric/Biological Unit (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)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZLH)

(-) 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:301
 aligned with CBPA1_BOVIN | P00730 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:303
                                   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   
          CBPA1_BOVIN   113 STNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTL 415
               SCOP domains d1zlha_ A: Carboxypeptidase A                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1zlhA00 A:3-305 Zn peptidases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------Peptidase_M14-1zlhA01 A:18-296                                                                                                                                                                                                                                                         --------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...........--......hhhhh..........................hhhhhhhhhhhhhhh.eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhhh.....eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------A----------------------------------------------------------------------------V SAPs(SNPs)
                    PROSITE ---------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT--------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zlh A   3 STNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVT--SLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVAALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTV 305
                                    12        22        32        42        52        62        72        82        92       102       112       122       132|  |   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   
                                                                                                                                                            133  |                                                                                                                                                                         
                                                                                                                                                               136                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with TCI1_RHIBU | Q5EPH2 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:74
                                    32        42        52        62        72        82        92    
           TCI1_RHIBU    23 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL  96
               SCOP domains d1zlhb1 B:1-37                       d1zlhb2 B:38-74                       SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains Inhibitor_I68-1zlhB01 B:1-74                                               Pfam domains
         Sec.struct. author hhhhhh..eeehhhhhhhh.ee.......eee.hhhh..hhhhh.eeee.......hhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1zlh B   1 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL  74
                                    10        20        30        40        50        60        70    

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (20, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 B   (TCI1_RHIBU | Q5EPH2)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    GO:0008191    metalloendopeptidase inhibitor activity    Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0044002    acquisition of nutrients from host    The process that begins with the production and formation of structures and molecules in an organism that are required for the acquisition and utilization of nutrients from its host organism, and the ends with the acquirement of the nutrients. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    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.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

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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 2abz 2ctb 2ctc 2rfh 3cpa 3fvl 3fx6 3i1u 3kgq 4cpa 5cpa 6cpa 7cpa 8cpa
        TCI1_RHIBU | Q5EPH21zli 2jto 2k2x 2k2y 2k2z 3d4u 3lms 3osl

(-) Related Entries Specified in the PDB File

1zli CRYSTAL STRUCTURE OF THE TICK CARBOXYPEPTIDASE INHIBITOR IN COMPLEX WITH HUMAN CARBOXYPEPTIDASE B