1FD4 Antimicrobial Peptide date Jul 19, 2000
title Human Beta-Defensin 2
authors D.M.Hoover, J.Lubkowski
compound source
Molecule: Beta-Defensin 2
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Synonym: Hbd-2, Skin-Antimicrobial Peptide 1
Engineered: Yes
Synthetic: Yes
Other_details: This Peptide Was Chemically Synthesized. The Sequence Of This Peptide Occurs Naturally In Humans (Homo Sapiens)
symmetry Space Group: P 1 21 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.525 79.950 74.271 90.00 105.30 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand SO4 enzyme
related structures by homologous chain: 1FD3, 1FQQ
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G
  • chemoattractant activity


  • Primary referenceThe structure of human beta-defensin-2 shows evidence of higher order oligomerization., Hoover DM, Rajashankar KR, Blumenthal R, Puri A, Oppenheim JJ, Chertov O, Lubkowski J, J Biol Chem 2000 Oct 20;275(42):32911-8. PMID:10906336
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (1fd4.pdb1.gz) 18 Kb
  • Biological Unit Coordinates (1fd4.pdb2.gz) 16 Kb
  • Biological Unit Coordinates (1fd4.pdb3.gz) 18 Kb
  • Biological Unit Coordinates (1fd4.pdb4.gz) 16 Kb
  • Biological Unit Coordinates (1fd4.pdb5.gz) 17 Kb
  • Biological Unit Coordinates (1fd4.pdb6.gz) 17 Kb
  • Biological Unit Coordinates (1fd4.pdb7.gz) 17 Kb
  • Biological Unit Coordinates (1fd4.pdb8.gz) 16 Kb
  • LPC: Ligand-Protein Contacts for 1FD4
  • CSU: Contacts of Structural Units for 1FD4
  • Likely Quarternary Molecular Structure file(s) for 1FD4
  • Structure Factors (427 Kb)
  • Retrieve 1FD4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1FD4 from S2C, [Save to disk]
  • Re-refined 1fd4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1FD4 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1FD4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1FD4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1fd4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1fd4b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1fd4c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1fd4d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1fd4e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1fd4f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1fd4g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1fd4h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1fd4i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1fd4j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1fd4k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1fd4l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1fd4m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1fd4n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1fd4o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1fd4p_, region P [Jmol] [rasmolscript] [script source]
  • Fold representative 1fd4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1fd4_B] [1fd4_A] [1fd4] [1fd4_J] [1fd4_O] [1fd4_C] [1fd4_E] [1fd4_D] [1fd4_H] [1fd4_G] [1fd4_L] [1fd4_N] [1fd4_K] [1fd4_I] [1fd4_M] [1fd4_P] [1fd4_F]
  • SWISS-PROT database: [O15263]
  • Belongs to the pore-forming -defensin (-defensin) family according to TCDB.
  • Domain organization of [DEFB2_HUMAN] by SWISSPFAM
  • Domain found in 1FD4: [DEFSN ] by SMART
  • Other resources with information on 1FD4
  • Community annotation for 1FD4 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1FD4 from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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