Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HUMAN BETA-DEFENSIN-1 (MUTANT GLN24ALA)
 
Authors :  J. Lubkowski, M. Pazgier
Date :  20 Oct 06  (Deposition) - 31 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.98
Chains :  Asym./Biol. Unit :  A
Keywords :  Antimicrobial, Chemotactic, Defensin, Mutant, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Pazgier, A. Prahl, D. M. Hoover, J. Lubkowski
Studies Of The Biological Properties Of Human Beta-Defensin 1.
J. Biol. Chem. V. 282 1819 2007
PubMed-ID: 17071614  |  Reference-DOI: 10.1074/JBC.M607210200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-DEFENSIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPAED4
    Expression System StrainBL21(DE3)PLYSE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHUMAN BETA-DEFENSIN 1, RESIDUES 33-68
    GeneDEFB1, BD1, HBD1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBD-1, DEFENSIN, BETA 1, HBD-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2NLS)

(-) Sites  (0, 0)

(no "Site" information available for 2NLS)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:34
2A:12 -A:27
3A:17 -A:35

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018405V38IDEFB1_HUMANPolymorphism2738047AV6I
2UniProtVAR_014925A48VDEFB1_HUMANPolymorphism1800967AA16V
3UniProtVAR_014926C67SDEFB1_HUMANPolymorphism1800968AC35S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002974391ENSE00001087806chr8:6735544-6735319226DEFB1_HUMAN1-21210--
1.2ENST000002974392ENSE00001087807chr8:6728348-6728097252DEFB1_HUMAN21-68481A:1-3636

(-) 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:36
 aligned with DEFB1_HUMAN | P60022 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:36
                                    42        52        62      
           DEFB1_HUMAN   33 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK 68
               SCOP domains d2nlsa_ A: automated matches         SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains Defensin_beta-2nlsA01 A:1-36         Pfam domains
         Sec.struct. author hhhhhhhhh.eee.........eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----I---------V------------------S- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-36 UniProt: 21-68 Transcript 1
                  2nls A  1 DHYNCVSSGGQCLYSACPIFTKIQGTCYRGEAKCCK 36
                                    10        20        30      

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Defensin (30)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEFB1_HUMAN | P60022)
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0002526    acute inflammatory response    Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0002227    innate immune response in mucosa    Any process of the innate immune response that takes place in the mucosal tissues.
    GO:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
    GO:0033574    response to testosterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2nls)
 
  Sites
(no "Sites" information available for 2nls)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2nls)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2nls
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DEFB1_HUMAN | P60022
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DEFB1_HUMAN | P60022
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DEFB1_HUMAN | P600221e4s 1iju 1ijv 1kj5 2nlb 2nlc 2nld 2nle 2nlf 2nlg 2nlh 2nlp 2nlq 2plz

(-) Related Entries Specified in the PDB File

2nlb HUMAN BETA-DEFENSIN-1 (MUTANT ASN4ALA)
2nlc HUMAN BETA-DEFENSIN-1 (MUTANT SER8ALA)
2nld HUMAN BETA-DEFENSIN-1 (MUTANT GLN11ALA)
2nle HUMAN BETA-DEFENSIN-1 (MUTANT GLN11ALA)
2nlf HUMAN BETA-DEFENSIN-1 (MUTANT LEU13GLU)
2nlh HUMAN BETA-DEFENSIN-1 (MUTANT GLN24ALA)
2nlp HUMAN BETA-DEFENSIN-1 (MUTANT GLN24GLU)
2nlq HUMAN BETA-DEFENSIN-1 (MUTANT LYS31ALA)