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(-) Description

Title :  SOLUTION STRUCTURE OF THE CATHELIN-LIKE DOMAIN OF PROTEGRINS (THE R87-P88 AND D118-P119 AMIDE BONDS ARE IN THE CIS CONFORMATION)
 
Authors :  Y. Yang, J. F. Sanchez, M. P. Strub, B. Brutscher, A. Aumelas
Date :  06 Nov 02  (Deposition) - 03 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Cathelin-Like Domain, Cathelicidin, Proline Isomerization, Cystatin Fold, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yang, J. F. Sanchez, M. P. Strub, B. Brutscher, A. Aumelas
Nmr Structure Of The Cathelin-Like Domain Of The Protegrin-3 Precursor
Biochemistry V. 42 4669 2003
PubMed-ID: 12705830  |  Reference-DOI: 10.1021/BI027133C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEGRINS
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATHELIN-LIKE DOMAIN
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: PROTEGRIN 1, PROTEGRIN 2, PROTEGRIN 3, PROTEGRIN 4, PROTEGRIN 5

 Structural Features

(-) Chains, Units

  
NMR Structure (15x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1N5H)

(-) Sites  (0, 0)

(no "Site" information available for 1N5H)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:85 -A:96
2A:107 -A:124

(-) Cis Peptide Bonds  (2, 30)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Arg A:87 -Pro A:88
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Asp A:118 -Pro A:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N5H)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CATHELICIDINS_1PS00946 Cathelicidins signature 1.PG4_PIG34-47  1A:34-47
2CATHELICIDINS_2PS00947 Cathelicidins signature 2.PG4_PIG78-100  1A:78-100

(-) Exons   (0, 0)

(no "Exon" information available for 1N5H)

(-) Sequences/Alignments

NMR Structure
   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:105
 aligned with PG4_PIG | P49933 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:105
                                    35        45        55        65        75        85        95       105       115       125     
              PG4_PIG    26 SASAQALSYREAVLRAVDRLNEQSSEANLYRLLELDQPPKADEDPGTPKPVSFTVKETVCPRPTRQPPELCDFKENGRVKQCVGTVTLDQIKDPLDITCNEVQGV 130
               SCOP domains d1n5ha_ A: Cathelicidin motif of protegrin-3                                                              SCOP domains
               CATH domains 1n5hA00 A:26-130  [code=3.10.450.10, no name defined]                                                     CATH domains
               Pfam domains -----Cathelicidins-1n5hA01 A:31-97                                      --------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh...eeeeeeee.............eeeeeeeeeeeee.................eeeeeeee..........eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------CATHELICIDINS_------------------------------CATHELICIDINS_2        ------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1n5h A  26 GSHMQALSYREAVLRAVDRLNEQSSEANLYRLLELDQPPKADEDPGTPKPVSFTVKETVCPRPTRQPPELCDFKENGRVKQCVGTVTLDQIKDPLDITCNEVQGV 130
                                    35        45        55        65        75        85        95       105       115       125
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Cystatin (20)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (PG4_PIG | P49933)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
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.

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  Cis Peptide Bonds
    Arg A:87 - Pro A:88   [ RasMol ]  
    Asp A:118 - Pro A:119   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PG4_PIG | P49933: 1n5p

(-) Related Entries Specified in the PDB File

1n5p STRUCTURE WITH ALL AMIDE BONDS INVOLVING PROLINE RESIDUES IN TRANS CONFORMATION