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 Diffraction	resolution	1.70 Å
ligand	SO4	enzyme
related structures	by homologous chain: 1FD3, 1FQQ
Gene Ontology	Chain Function Process Component F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G chemoattractant activity
Primary reference	The 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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