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(-) Description

Title :  .98A CRYSTAL STRUCTURE OF A DIMERIC PLANT DEFENSIN SPE10
 
Authors :  H. Zhou, X. Song, W. Gong
Date :  01 Dec 10  (Deposition) - 29 Dec 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimer, Defensin, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhou, X. Song, W. Gong
0. 98A Crystal Structure Of A Dimeric Plant Defensin Spe10
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEFENSIN
    Chains: A, B
    Organism Common: JICAMA,POTATO-BEAN,YAM-BEAN
    Organism Scientific: PACHYRHIZUS EROSUS
    Organism Taxid: 109171
    Synonym: SPE10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3PSM)

(-) Sites  (0, 0)

(no "Site" information available for 3PSM)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:47
2A:14 -A:35
3A:20 -A:41
4A:24 -A:43
5B:3 -B:47
6B:14 -B:35
7B:20 -B:41
8B:24 -B:43

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PSM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PSM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PSM)

(-) Exons   (0, 0)

(no "Exon" information available for 3PSM)

(-) 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:47
 aligned with Q6B519_9FABA | Q6B519 from UniProtKB/TrEMBL  Length:47

    Alignment length:47
                                    10        20        30        40       
          Q6B519_9FABA    1 KTCENLADTFRGPCFTDGSCDDHCKNKEHLIKGRCRDDFRCWCTRNC 47
               SCOP domains d3psma_ A: automated matches                    SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.........hhhhhhhhhhhh....eeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  3psm A  1 KTCENLADTFRGPCFTDGSCDDHCKNKEHLIKGRCRDDFRCWCTRNC 47
                                    10        20        30        40       


Chain B from PDB  Type:PROTEIN  Length:47
 aligned with Q6B519_9FABA | Q6B519 from UniProtKB/TrEMBL  Length:47

    Alignment length:47
                                    10        20        30        40       
          Q6B519_9FABA    1 KTCENLADTFRGPCFTDGSCDDHCKNKEHLIKGRCRDDFRCWCTRNC 47
               SCOP domains d3psmb_ B: automated matches                    SCOP domains
               CATH domains ----------------------------------------------- CATH domains
           Pfam domains (1) Gamma-thionin-3psmB01 B:1-47                    Pfam domains (1)
           Pfam domains (2) Gamma-thionin-3psmB02 B:1-47                    Pfam domains (2)
         Sec.struct. author .eeeee.........hhhhhhhhhhhh....eeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  3psm B  1 KTCENLADTFRGPCFTDGSCDDHCKNKEHLIKGRCRDDFRCWCTRNC 47
                                    10        20        30        40
   Legend:   → Mismatch (orange background)
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    → 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, 2)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PSM)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Knottin_1 (78)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6B519_9FABA | Q6B519)
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:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.

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