Interesting Structures

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A list of selected protein structures, with defined characteristics, that might be of interest for teaching, testing, etc Original list from [1]

  • Cyclic polymers (1sfi, 6dny, 1hvz)
  • B-DNA (1bna)
  • Missing carbonyl oxygen (1gfl)
  • Mono-saccharides with alt locs (1b5f)
  • Microheterogeneity
Protein (1ejg, 3nir)
DNA (3vok)
  • PNA: peptide nucleic acid (5eme, 1xj9)
  • Peptide derived residues
GFP chromophores (5z6y)
  • Nucleotides that don’t have a parent base set, i.e. detect purine/pyrimidine from geometry (THX in 1aul, OMC in e.g. 5d3g)
  • Bases with modified ring atoms
DZ has C1 instead of N1 (e.g. 6i4n)
DP has N5 instead of C5 and C7 instead of N7 (e.g. 6i4n)
  • Beta & Gamma peptides (e.g. 1gac, 6pqf)
  • Mixed (heterogeneous) all-atom/trace-only RNA model (1jgq)
  • Polymers with residues with missing trace atoms (e.g. 2qfj)
  • Modified RNA bases (1y26, 5l4o)
  • Discontinuous chains, i.e. gaps in the sequence (3sn6)
  • Lots of sheets (1cbs)
  • DNA (2np2, 1d66)
  • C-alpha only (2rcj)
  • Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6sw3)
  • Close backbone atoms but not linked (e.g. 4hiv)
  • Non-standard residues
Protein (1brr, 5z6y)
DNA (5d3g)
  • Multiple models with different sets of ligands or missing ligands (1j6t, 1vrc, 2icy, 1o2f)

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Jaime Prilusky

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