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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEXAMERIC ANTI-MICROBIAL PEPTIDE CHANNEL DERMCIDIN
 
Authors :  K. Zeth
Date :  09 Oct 12  (Deposition) - 17 Oct 12  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Antibiotic, Anti-Microbial Peptide Channel, Membrane Spanning Peptide, Human Epidermal Surface (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Song, C. Weichbrodt, E. S. Salnikov, M. Dynowski, B. O. Forsberg, B. Bechinger, C. Steinem, B. L. De Groot, U. Zachariae, K. Zeth
Crystal Structure And Functional Mechanism Of A Human Antimicrobial Membrane Channel.
Proc. Natl. Acad. Sci. Usa V. 110 4586 2013
PubMed-ID: 23426625  |  Reference-DOI: 10.1073/PNAS.1214739110

(-) Compounds

Molecule 1 - DCD-1
    Chains: A, B, C
    EC Number: 3.4.-.-
    Fragment: PEPTIDE, RESIDUES 63-110
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PEPTIDE OF 48 RESIDUES
    Synonym: DERMCIDIN, PREPROTEOLYSIN, SURVIVAL-PROMOTING PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:38 , ASP A:42 , GLU B:5 , ASP B:9BINDING SITE FOR RESIDUE ZN A1049
2AC2SOFTWAREGLU A:5 , ASP A:9 , HIS B:38 , ASP B:42BINDING SITE FOR RESIDUE ZN B1049
3AC3SOFTWAREGLU C:5 , ASP C:9 , HIS C:38 , ASP C:42BINDING SITE FOR RESIDUE ZN C1049
4AC4SOFTWAREASP A:24 , ASP A:28 , HOH A:2003 , LYS B:6 , LYS B:20BINDING SITE FOR RESIDUE ZN A1050
5AC5SOFTWAREASP B:24 , ASP B:28 , HOH B:2002 , HOH B:2009BINDING SITE FOR RESIDUE ZN B1050
6AC6SOFTWAREASP C:24 , ASP C:28 , HOH C:2005BINDING SITE FOR RESIDUE ZN C1050

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YMK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YMK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YMK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YMK)

(-) Exons   (0, 0)

(no "Exon" information available for 2YMK)

(-) Sequences/Alignments

Asymmetric 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 DCD_HUMAN | P81605 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:46
                                    74        84        94       104      
            DCD_HUMAN    65 LLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSVL 110
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 2ymk A   3 LLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSVL  48
                                    12        22        32        42      


Chain B from PDB  Type:PROTEIN  Length:47
 aligned with DCD_HUMAN | P81605 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:47
                                    73        83        93       103       
            DCD_HUMAN    64 SLLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSVL 110
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 2ymk B   2 SLLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSVL  48
                                    11        21        31        41       


Chain C from PDB  Type:PROTEIN  Length:47
 aligned with DCD_HUMAN | P81605 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:47
                                    73        83        93       103       
            DCD_HUMAN    64 SLLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSVL 110
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 2ymk C   2 SLLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSVL  48
                                    11        21        31        41
   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  (0, 0)

(no "SCOP Domain" information available for 2YMK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YMK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YMK)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DCD_HUMAN | P81605)
molecular function
    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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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: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.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

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 Related Entries

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

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        DCD_HUMAN | P81605: 2ksg 2ndk

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