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(-) Description

Title :  HUMAN BETA-DEFENSIN 2
 
Authors :  D. M. Hoover, J. Lubkowski
Date :  19 Jul 00  (Deposition) - 01 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Defensin, Human Beta-Defensin 2, Beta-Defensin, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. M. Hoover, K. R. Rajashankar, R. Blumenthal, A. Puri, J. J. Oppenheim, O. Chertov, J. Lubkowski
The Structure Of Human Beta-Defensin-2 Shows Evidence Of Higher Order Oligomerization.
J. Biol. Chem. V. 275 32911 2000
PubMed-ID: 10906336  |  Reference-DOI: 10.1074/JBC.M006098200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-DEFENSIN 2
    ChainsA, B, C, D
    EngineeredYES
    Other DetailsTHIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
    SynonymHBD-2, SKIN-ANTIMICROBIAL PEPTIDE 1
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:83 , LYS D:10 , PHE D:19 , CYS D:20 , LYS D:36 , HOH D:216 , HOH D:223 , HOH D:225 , HOH D:231BINDING SITE FOR RESIDUE SO4 D 195

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:8 -A:37
2A:15 -A:30
3A:20 -A:38
4B:8 -B:37
5B:15 -B:30
6B:20 -B:38
7C:8 -C:37
8C:15 -C:30
9C:20 -C:38
10D:8 -D:37
11D:15 -D:30
12D:20 -D:38

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FD3)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003181571ENSE00001753483chr8:7274385-727429294DFB4A_HUMAN1-20200--
1.2ENST000003181572ENSE00001646530chr8:7272619-7272382238DFB4A_HUMAN20-64454A:1-41
B:1-40
C:1-40
D:1-41
41
40
40
41

(-) 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:41
 aligned with DFB4A_HUMAN | O15263 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:41
                                    33        43        53        63 
           DFB4A_HUMAN   24 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKKP 64
               SCOP domains d1fd3a_ A: Beta-defensin, BD              SCOP domains
               CATH domains 1fd3A00 A:1-41                            CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..eee........eeee.......eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:1-41 UniProt: 20-64      Transcript 1
                  1fd3 A  1 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKKP 41
                                    10        20        30        40 

Chain B from PDB  Type:PROTEIN  Length:40
 aligned with DFB4A_HUMAN | O15263 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:40
                                    33        43        53        63
           DFB4A_HUMAN   24 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKK 63
               SCOP domains d1fd3b_ B: Beta-defensin, BD             SCOP domains
               CATH domains 1fd3B00 B:1-40                           CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..eee........eeee.......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:1-40 UniProt: 20-64     Transcript 1
                  1fd3 B  1 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKK 40
                                    10        20        30        40

Chain C from PDB  Type:PROTEIN  Length:40
 aligned with DFB4A_HUMAN | O15263 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:40
                                    33        43        53        63
           DFB4A_HUMAN   24 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKK 63
               SCOP domains d1fd3c_ C: Beta-defensin, BD             SCOP domains
               CATH domains 1fd3C00 C:1-40                           CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..eeee.......eeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: C:1-40 UniProt: 20-64     Transcript 1
                  1fd3 C  1 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKK 40
                                    10        20        30        40

Chain D from PDB  Type:PROTEIN  Length:41
 aligned with DFB4A_HUMAN | O15263 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:41
                                    33        43        53        63 
           DFB4A_HUMAN   24 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKKP 64
               SCOP domains d1fd3d_ D: Beta-defensin, BD              SCOP domains
               CATH domains 1fd3D00 D:1-41                            CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhh..eee........eeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: D:1-41 UniProt: 20-64      Transcript 1
                  1fd3 D  1 GIGDPVTCLKSGAICHPVFCPRRYKQIGTCGLPGTKCCKKP 41
                                    10        20        30        40 

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FD3)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DFB4A_HUMAN | O15263)
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: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: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.
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: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)

UniProtKB/Swiss-Prot
        DFB4A_HUMAN | O152631e4q 1fd4 1fqq

(-) Related Entries Specified in the PDB File

1fd4 HUMAN BETA-DEFENSIN 2, MONOCLINIC