Interesting Structures

From Proteopedia

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)