1DN3	De Novo Protein	date	Dec 16, 1999
title	Nmr Structure Of A Model Hydrophilic Amphipathic Helical Basic Peptide
authors	R.Montserret, M.J.Mcleish, A.Bockmann, C.Geourjon, F.Penin
compound		source
Molecule: Gln-Ala-Pro-Ala-Tyr-Lys-Lys-Ala-Ala-Lys-Lys-Leu- Ala-Glu-Ser; Chain: A Fragment: Human Platelet Factor 4, Segment 59-73 Mutation: Yes Other_details: Chemically Synthesized		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Other_details: Human Platelet Factor 4 With Mutations (L62a I66a, I67a, L71a) Chemically Synthesized
method	Solution NMR
Gene Ontology	Chain Function Process Component A cytokine activity chemokine activity heparin binding platelet degranulation chemotaxis blood coagulation positive regulation of gene ... positive regulation of macro... negative regulation of angio... cytokine-mediated signaling ... platelet activation leukocyte chemotaxis positive regulation of tumor... negative regulation of apopt... negative regulation of MHC c... positive regulation of macro... negative regulation of megak... negative regulation of cytol... extracellular region extracellular space platelet alpha granule lumen...
Primary reference	Involvement of electrostatic interactions in the mechanism of peptide folding induced by sodium dodecyl sulfate binding., Montserret R, McLeish MJ, Bockmann A, Geourjon C, Penin F, Biochemistry 2000 Jul 25;39(29):8362-73. PMID:10913242

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (7 Kb) [Save to disk] CSU: Contacts of Structural Units for 1DN3 Original NMR restraints for 1DN3 from PDB Retrieve 1DN3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DN3 from S2C, [Save to disk]

View 1DN3 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1DN3

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1DN3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dn3a_, region A [Jmol] [rasmolscript] [script source] Fold representative 1dn3 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1dn3_A] SWISS-PROT database: [P02776] Domain organization of [PLF4_HUMAN] by SWISSPFAM Alignments of the sequence of 1DN3 with the sequences similar proteins can be viewed for 1DN3's classification [PLF4_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [PLF4_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1DN3

Community annotation for 1DN3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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