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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF NICOTIANA ALATA DEFENSIN NAD1
 
Authors :  G. D. Mills, F. T. Lay, M. D. Hulett, M. Kvansakul
Date :  06 Dec 11  (Deposition) - 25 Apr 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antimicrobial Protein, Innate Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. T. Lay, G. D. Mills, I. K. Poon, N. P. Cowieson, N. Kirby, A. A. Baxter, N. L. Van Der Weerden, C. Dogovski, M. A. Perugini, M. A. Anderson, M. Kvansakul, M. D. Hulett
Dimerization Of Plant Defensin Nad1 Enhances Its Antifungal Activity.
J. Biol. Chem. V. 287 19961 2012
PubMed-ID: 22511788  |  Reference-DOI: 10.1074/JBC.M111.331009

(-) Compounds

Molecule 1 - FLOWER-SPECIFIC DEFENSIN
    Chains: A, B
    Fragment: RESIDUES 26-72
    Organ: FLOWER
    Organism Common: ORNAMENTAL TOBACCO
    Organism Scientific: NICOTIANA ALATA
    Organism Taxid: 4087
    Synonym: NAD1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:35 , LYS A:36 , ILE A:37 , LEU A:38 , HOH A:2038 , HOH A:2042 , ARG B:1BINDING SITE FOR RESIDUE PO4 A1048
2AC2SOFTWARELYS B:22 , SER B:26 , HOH B:2020 , HOH B:2034BINDING SITE FOR RESIDUE PO4 B1048

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:47
2A:14 -A:34
3A:20 -A:41
4A:24 -A:43
5B:3 -B:47
6B:14 -B:34
7B:20 -B:41
8B:24 -B:43

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AB0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AB0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAMMA_THIONINPS00940 Gamma-thionins family signature.DEF_NICAL26-49  1B:1-24

(-) Exons   (0, 0)

(no "Exon" information available for 4AB0)

(-) 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:46
 aligned with DEF_NICAL | Q8GTM0 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:46
                                    36        46        56        66      
             DEF_NICAL   27 ECKTESNTFPGICITKPPCRKACISEKFTDGHCSKILRRCLCTKPC 72
               SCOP domains d4ab0a_ A: Floral defensin 1                   SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........hhhhhhhhhhhh...eeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE GAMMA_THIONIN  PDB: -  ----------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  4ab0 A  2 ECKTESNTFPGICITKPPCRKACISEKFTDGHCSKILRRCLCTKPC 47
                                    11        21        31        41      


Chain B from PDB  Type:PROTEIN  Length:47
 aligned with DEF_NICAL | Q8GTM0 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:47
                                    35        45        55        65       
             DEF_NICAL   26 RECKTESNTFPGICITKPPCRKACISEKFTDGHCSKILRRCLCTKPC 72
               SCOP domains d4ab0b_ B: Floral defensin 1                    SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhh...eeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE GAMMA_THIONIN           ----------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  4ab0 B  1 RECKTESNTFPGICITKPPCRKACISEKFTDGHCSKILRRCLCTKPC 47
                                    10        20        30        40
   Legend:   → Mismatch (orange background)
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  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 4AB0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AB0)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEF_NICAL | Q8GTM0)
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.
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.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_NICAL | Q8GTM0: 4aaz 4cqk

(-) Related Entries Specified in the PDB File

4aaz X-RAY STRUCTURE OF NICOTIANA ALATA DEFENSIN 1 NAD1