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(-) Description

Title :  STRUCTURE OF THE COMPLEX BETWEEN SMCI AND HUMAN CARBOXYPEPTIDASE A4
 
Authors :  M. Alonso-Del-Ribero, M. L. Reytor, S. A. Trejo, M. A. Chavez, F. X. Avil D. Reverter
Date :  05 Oct 12  (Deposition) - 17 Jul 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-Hydrolase Inhibitor Complex, Serine Protease Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Alonso Del Rivero, M. L. Reytor, S. A. Trejo, M. A. Chavez, F. X. Aviles, D. Reverter
A Noncanonical Mechanism Of Carboxypeptidase Inhibition Revealed By The Crystal Structure Of The Tri-Kunitz Smci In Complex With Human Cpa4.
Structure V. 21 1118 2013
PubMed-ID: 23746805  |  Reference-DOI: 10.1016/J.STR.2013.04.021

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE A4
    ChainsA
    EC Number3.4.17.-
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICZAA
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentRESIDUES 112-421
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCARBOXYPEPTIDASE A3
 
Molecule 2 - CARBOXYPEPTIDASE INHIBITOR SMCI
    ChainsB
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICZAA
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificSABELLASTARTE MAGNIFICA
    Organism Taxid389514
    SynonymSMCI INHIBITOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , HOH A:2032 , ILE B:1BINDING SITE FOR RESIDUE ZN A 500

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:138 -A:161
2B:4 -B:54
3B:13 -B:37
4B:29 -B:50
5B:56 -B:106
6B:65 -B:89
7B:81 -B:102
8B:115 -B:165
9B:124 -B:148
10B:140 -B:161

(-) 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_020393P157TCBPA4_HUMANPolymorphism3735051AP45T
2UniProtVAR_048595R183LCBPA4_HUMANPolymorphism3735053AR71L
3UniProtVAR_020394G303CCBPA4_HUMANPolymorphism2171492AG191C

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

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.PCPI_SABMA4-54
56-106
115-165
  3B:4-54
B:56-106
B:115-165
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.PCPI_SABMA32-50
84-102
143-161
  3B:32-50
B:84-102
B:143-161
3CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPA4_HUMAN172-194  1A:60-82
4CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPA4_HUMAN308-318  1A:196-206

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002224821aENSE00001175329chr7:129932993-12993308896CBPA4_HUMAN1-23230--
1.3ENST000002224823ENSE00000882290chr7:129938586-12993866782CBPA4_HUMAN23-50280--
1.4aENST000002224824aENSE00000723226chr7:129939110-129939244135CBPA4_HUMAN51-95450--
1.6ENST000002224826ENSE00000723228chr7:129940656-12994075499CBPA4_HUMAN96-128331A:5-1612
1.7cENST000002224827cENSE00000723230chr7:129944318-129944419102CBPA4_HUMAN129-162341A:17-5034
1.8bENST000002224828bENSE00000723233chr7:129945656-129945760105CBPA4_HUMAN163-197351A:51-8535
1.9cENST000002224829cENSE00000723234chr7:129946627-129946737111CBPA4_HUMAN198-234371A:86-12237
1.10bENST0000022248210bENSE00000723236chr7:129948147-12994823791CBPA4_HUMAN235-265311A:123-15331
1.11ENST0000022248211ENSE00000723239chr7:129950627-129950826200CBPA4_HUMAN265-331671A:153-21967
1.12ENST0000022248212ENSE00000723240chr7:129951878-12995196285CBPA4_HUMAN332-360291A:220-24829
1.13bENST0000022248213bENSE00001279439chr7:129962329-1299640191691CBPA4_HUMAN360-421621A:248-30861

(-) 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 CBPA4_HUMAN | Q9UI42 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:304
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416    
          CBPA4_HUMAN   117 NFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL 420
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee.........eeeeee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhhh.eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------T-------------------------L-----------------------------------------------------------------------------------------------------------------------C--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6    Exon 1.7c  PDB: A:17-50           Exon 1.8b  PDB: A:51-85            Exon 1.9c  PDB: A:86-122             Exon 1.10b  PDB: A:123-153     ------------------------------------------------------------------Exon 1.12  PDB: A:220-248    ------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: A:153-219 UniProt: 265-331                         ----------------------------Exon 1.13b  PDB: A:248-308 UniProt: 360-421 [INCOMPLETE]      Transcript 1 (2)
                 4bd9 A   5 NFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL 308
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with PCPI_SABMA | P84875 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
           PCPI_SABMA     1 ISVCDLPADRGQCTAYIPQWFFNKTTEDCEKFVYGGCQGNANRFETKDDCIANCGCNLPSKVGPCRVSARMWFHNPETEKCEVFIYGGCHGNANRFATETECQEVCDRYQKPGFCYQPSETGPCKGSFPRYYYDYEDGECKEFIYGGCEGNANNFETKESCENAC 165
               SCOP domains d4bd9b1 B:1-54 automated matches                      d4bd9b2 B:55-109 automated matches                     d4bd9b3 B:110-165 automated matches                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..........eeeeeee....eeeeeee...........hhhhhhhhhh.............eeeeeee....eeeeeee...........hhhhhhhhhh....hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---BPTI_KUNITZ_2  PDB: B:4-54 UniProt: 4-54           -BPTI_KUNITZ_2  PDB: B:56-106 UniProt: 56-106       --------BPTI_KUNITZ_2  PDB: B:115-165 UniProt: 115-165      PROSITE (1)
                PROSITE (2) -------------------------------BPTI_KUNITZ_1      ---------------------------------BPTI_KUNITZ_1      ----------------------------------------BPTI_KUNITZ_1      ---- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bd9 B   1 ISVCDLPADRGQCTAYIPQWFFAKTTEDCEKFVYGGCQGNANRFETKDDCIANCGCNLPSKVGPCRVSARMWFHNPETEKCEVFIYGGCHGNANRFATETECQEVCDRYQKPGFCYQPSETGPCKGSFPRYYYDYEDGECKEFIYGGCEGNANNFETKESCENAC 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     

   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  (1, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BD9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BD9)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPA4_HUMAN | Q9UI42)
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:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.
    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   (PCPI_SABMA | P84875)
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.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBPA4_HUMAN | Q9UI422bo9 2boa 2pcu 4a94

(-) Related Entries Specified in the PDB File

2bo9 HUMAN CARBOXYPEPTIDASE A4 IN COMPLEX WITH HUMAN LATEXIN.
2boa HUMAN PROCARBOXYPEPTIDASE A4.
4a94 STRUCTURE OF THE CARBOXYPEPTIDASE INHIBITOR FROM NERITA VERSICOLOR IN COMPLEX WITH HUMAN CPA4