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(-) Description

Title :  STRUCTURE OF CYCLOTIDE KALATA B1 IN DPC MICELLES SOLUTION
 
Authors :  Z. O. Shenkarev, K. D. Nadezhdin, V. A. Sobol, A. G. Sobol, L. Skjeldal, A. S. Arseniev
Date :  12 May 05  (Deposition) - 25 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cyclotide, Cyclic Peptide, Knottin, Cystine Knot, Antimicrobial Peptide, Plant Protein, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. O. Shenkarev, K. D. Nadezhdin, V. A. Sobol, A. G. Sobol, L. Skjeldal, A. S. Arseniev
Conformation And Mode Of Membrane Interaction In Cyclotides. Spatial Structure Of Kalata B1 Bound To A Dodecylphosphocholine Micelle.
Febs J. V. 273 2658 2006
PubMed-ID: 16817894  |  Reference-DOI: 10.1111/J.1742-4658.2006.05282.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KALATA B1
    Chains: A
    Organism Scientific: OLDENLANDIA AFFINIS
    Organism Taxid: 60225

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1ZNU)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:1 -A:15
2A:5 -A:17
3A:10 -A:22

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Trp A:19 -Pro A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYCLOTIDE_MOEBIUSPS60009 Cyclotides Moebius subfamily signature.KAB4_OLDAF5-14  1A:1-10
KAB1_OLDAF93-102  1A:1-10

(-) Exons   (0, 0)

(no "Exon" information available for 1ZNU)

(-) 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:29
 aligned with KAB1_OLDAF | P56254 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:29
                                   102       112         
           KAB1_OLDAF    93 CGETCVGGTCNTPGCTCSWPVCTRNGLPS 121
               SCOP domains d1znua_ A: Kalata B1          SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains Cyclotide-1znuA01 A:1-25 ---- Pfam domains
         Sec.struct. author ..............eeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE CYCLOTIDE_------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 1znu A   1 CGETCVGGTCNTPGCTCSWPVCTRNGLPV  29
                                    10        20         


Chain A from PDB  Type:PROTEIN  Length:29
 aligned with KAB4_OLDAF | P83938 from UniProtKB/Swiss-Prot  Length:29

    Alignment length:29
                                                   29    
                                    14        24    |    
           KAB4_OLDAF     5 CGETCVGGTCNTPGCTCSWPVCTRD----   -
               SCOP domains d1znua_ A: Kalata B1          SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains Cyclotide-1znuA01 A:1-25 ---- Pfam domains
         Sec.struct. author ..............eeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE CYCLOTIDE_------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 1znu A   1 CGETCVGGTCNTPGCTCSWPVCTRNGLPV  29
                                    10        20
   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: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZNU)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Cyclotide] (21)

(-) Gene Ontology  (4, 5)

NMR Structure(hide GO term definitions)
Chain A   (KAB1_OLDAF | P56254)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    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.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.

Chain A   (KAB4_OLDAF | P83938)
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.

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  Cis Peptide Bonds
    Trp A:19 - Pro A:20   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAB1_OLDAF | P56254: 1jjz 1k48 1kal 1n1u 1nb1 1orx 2f2i 2f2j 2jue 2khb 2mh1 2mn1 4ttm 4ttn 4tto

(-) Related Entries Specified in the PDB File

6627
1jjz STRUCTURE OF KB1 (LADDER)
1kal FIRST STRUCTURE OF KB1 (KNOT)
1nb1 REFINED STRUCTURE OF KB1 (KNOT)