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
methodSolution NMR
Primary referenceInvolvement 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.
  • 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] [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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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