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(-) Description

Title :  CRYSTAL STRUCTURE OF CARBOXYPEPTIDASE Y INHIBITOR COMPLEXED WITH THE COGNATE PROTEINASE
 
Authors :  J. Mima, M. Hayashida, T. Fujii, Y. Narita, R. Hayashi, M. Ueda, Y. Hata
Date :  14 Sep 04  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Carboxypeptidase Inhibitor, Serine Proteinase Inhibitor, Proteinase- Inhibitor Complex, Phosphatidylethanolamine-Binding Protein, Phospholipid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Mima, M. Hayashida, T. Fujii, Y. Narita, R. Hayashi, M. Ueda, Y. Hata
Structure Of The Carboxypeptidase Y Inhibitor I(C) In Complex With The Cognate Proteinase Reveals A Novel Mode Of The Proteinase-Protein Inhibitor Interaction
J. Mol. Biol. V. 346 1323 2005
PubMed-ID: 15713484  |  Reference-DOI: 10.1016/J.JMB.2004.12.051

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE Y
    ChainsA
    EC Number3.4.16.5
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymCARBOXYPEPTIDASE YSCY
 
Molecule 2 - CARBOXYPEPTIDASE Y INHIBITOR
    ChainsB
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymCPY INHIBITOR, IC, IC, DKA1 PROTEIN, NSP1 PROTEIN, TFS1 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:39 , ASN A:87 , HIS A:416 , HOH A:1034BINDING SITE FOR RESIDUE NAG A 810
2AC2SOFTWAREASN A:166 , ASN A:168BINDING SITE FOR RESIDUE NDG A 820
3AC3SOFTWAREASN A:368BINDING SITE FOR RESIDUE NDG A 830
4AC4SOFTWAREGLY A:52 , GLY A:53 , SER A:146 , TYR A:256 , HIS A:397 , HOH A:1000 , ACE B:500 , MET B:501BINDING SITE FOR RESIDUE SO4 A 901
5AC5SOFTWAREASP B:595 , PHE B:609 , HIS B:611 , ALA B:653 , PRO B:654 , HIS B:661 , TYR B:663BINDING SITE FOR RESIDUE SO4 B 902

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:56 -A:298
2A:193 -A:207
3A:217 -A:240
4A:224 -A:233
5A:262 -A:268

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:53 -Pro A:54
2Gln A:95 -Pro A:96
3Ala B:598 -Pro B:599

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WPX)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PBPPS01220 Phosphatidylethanolamine-binding protein family signature.CPYI_YEAST89-111  1B:589-611
2CARBOXYPEPT_SER_SERPS00131 Serine carboxypeptidases, serine active site.CBPY_YEAST253-260  1A:142-149
3CARBOXYPEPT_SER_HISPS00560 Serine carboxypeptidases, histidine active site.CBPY_YEAST498-515  1A:387-404

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR178C1YLR178C.1XII:513823-513164660CPYI_YEAST1-2192191B:501-719 (gaps)219

2.1YMR297W1YMR297W.1XIII:861921-8635191599CBPY_YEAST1-5325321A:1-421421

(-) 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:421
 aligned with CBPY_YEAST | P00729 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:421
                                   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 
           CBPY_YEAST   112 KIKDPKILGIDPNVTQYTGYLDVEDEDKHFFFWTFESRNDPAKDPVILWLNGGPGCSSLTGLFFELGPSSIGPDLKPIGNPYSWNSNATVIFLDQPVNVGFSYSGSSGVSNTVAAGKDVYNFLELFFDQFPEYVNKGQDFHIAGESYAGHYIPVFASEILSHKDRNFNLTSVLIGNGLTDPLTQYNYYEPMACGEGGEPSVLPSEECSAMEDSLERCLGLIESCYDSQSVWSCVPATIYCNNAQLAPYQRTGRNVYDIRKDCEGGNLCYPTLQDIDDYLNQDYVKEAVGAEVDHYESCNFDINRNFLFAGDWMKPYHTAVTDLLNQDLPILVYAGDKDFICNWLGNKAWTDVLPWKYDEEFASQKVRNWTASITDEVAGEVKSYKHFTYLRVFNGGHMVPFDVPENALSMVNEWIHGGFSL 532
               SCOP domains d1wpxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1wpxA01 A:1-180,A:253-421  [code=3.40.50.1820, no name defined]                                                                                                                     1wpxA02 A:181-252  [code=1.10.287.410, no name defined]                 1wpxA01 A:1-180,A:253-421  [code=3.40.50.1820, no name defined]                                                                                                           CATH domains
               Pfam domains ----Peptidase_S10-1wpxA01 A:5-417                                                                                                                                                                                                                                                                                                                                                                                                ---- Pfam domains
         Sec.struct. author .eehhhhh.......eeeeeee......eeeeeee..........eeeee.......hhhhhhh....eee.....eee...hhhhh.eeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh........eeeee....hhhhhh.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh........hhhhhhhhhh...eeeeee......hhhhhhhhhhhh...hhhhhhhh..eeee......eeeeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------CARBOXYP---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI----------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:1-421 UniProt: 1-532 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                    Transcript 2
                 1wpx A   1 KIKDPKILGIDPNVTQYTGYLDVEDEDKHFFFWTFESRNDPAKDPVILWLNGGPGCSSLTGLFFELGPSSIGPDLKPIGNPYSWNSNATVIFLDQPVNVGFSYSGSSGVSNTVAAGKDVYNFLELFFDQFPEYVNKGQDFHIAGESYAGHYIPVFASEILSHKDRNFNLTSVLIGNGLTDPLTQYNYYEPMACGEGGEPSVLPSEECSAMEDSLERCLGLIESCYDSQSVWSCVPATIYCNNAQLAPYQRTGRNVYDIRKDCEGGNLCYPTLQDIDDYLNQDYVKEAVGAEVDHYESCNFDINRNFLFAGDWMKPYHTAVTDLLNQDLPILVYAGDKDFICNWLGNKAWTDVLPWKYDEEFASQKVRNWTASITDEVAGEVKSYKHFTYLRVFNGGHMVPFDVPENALSMVNEWIHGGFSL 421
                                    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 

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with CPYI_YEAST | P14306 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:220
                             1                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
           CPYI_YEAST     - -MNQAIDFAQASIDSYKKHGILEDVIHDTSFQPSGILAVEYSSSAPVAMGNTLPTEKARSKPQFQFTFNKQMQKSVPQANAYVPQDDDLFTLVMTDPDAPSKTDHKWSEFCHLVECDLKLLNEATHETSGATEFFASEFNTKGSNTLIEYMGPAPPKGSGPHRYVFLLYKQPKGVDSSKFSKIKDRPNWGYGTPATGVGKWAKENNLQLVASNFFYAETK 219
               SCOP domains -d1wpxb1 B:501-719 Carboxypeptidase Y inhibitor                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------PBP-1wpxB01 B:533-715                                                                                                                                                                  ---- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeee..eee......hhhhhh...eeeeeee....------..........eeeeeee.............eeeeeeeeeee..---------..eeeeeee....eeee.............eeeeeeeee.....hhhhh.....hhhhhh.....hhhhhhhh...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------PBP  PDB: B:589-611    ------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 -Exon 1.1  PDB: B:501-719 (gaps) UniProt: 1-219                                                                                                                                                                              Transcript 1
                 1wpx B 500 xMNQAIDFAQASIDSYKKHGILEDVIHDTSFQPSGILAVEYSSSAPVAMGNTLPTEKARSKPQFQFTFNKQMQ------NAYVPQDDDLFTLVMTDPDAPSKTDHKWSEFCHLVECDLKLLN---------TEFFASEFNTKGSNTLIEYMGPAPPKGSGPHRYVFLLYKQPKGVDSSKFSKIKDRPNWGYGTPATGVGKWAKENNLQLVASNFFYAETK 719
                            |      509       519       529       539       549       559       569  |    579       589       599       609       619 |       - |     639       649       659       669       679       689       699       709       719
                          500-ACE                                                                 572    579                                       621       631                                                                                        

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPY_YEAST | P00729)
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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004185    serine-type carboxypeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0046938    phytochelatin biosynthetic process    The chemical reactions and pathways resulting in the formation of phytochelatins, any of a group of peptides that bind metals (Cd, Zn, Cu, Pb, Hg) in thiolate coordination complexes. The structure is of the type (gamma-glutamyl-cysteinyl)n-glycine, where n is 2 to 11.
    GO:0007039    protein catabolic process in the vacuole    The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
cellular component
    GO:0000324    fungal-type vacuole    A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Chain B   (CPYI_YEAST | P14306)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    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.
    GO:0046578    regulation of Ras protein signal transduction    Any process that modulates the frequency, rate or extent of Ras protein signal transduction.
    GO:0030162    regulation of proteolysis    Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000328    fungal-type vacuole lumen    The volume enclosed within the vacuolar membrane of a vacuole, the shape of which correlates with cell cycle phase. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.

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 Related Entries

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

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        CBPY_YEAST | P007291cpy 1ysc

(-) Related Entries Specified in the PDB File

1a44 1bd9 1beh 1fjj 1fux 1qou