Interesting PDB Entries
- 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
- 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)
- Helices of D-amino acids (e.g. 7QDI)
- 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)
- Collagen (6JEC)
- Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
- Long linear sugar chain (4HG6)
- Anisotropic B-factors/Ellipsoids (1EJG)
- NOS bridges (LYS-CSO in 7B0L, 6ZWJ, 6ZWH)
- Non-polymer components in polymer entities
- PN2 in 1F80
- ACE (many, e.g. 5AGU, 1E1X)
- ACY in 7ABY
- NH2 (many, e.g. 6Y13)
- Ligands with many rings
- STU (e.g. 1U59) - many fused rings
- HT (e.g. 127D) - rings connected by a single bond
- J2C (e.g. 7EFJ) - rings connected by a single atom
- RBF (e.g. 7QF2) - three linearly fused rings
- TA1 (e.g. 1JFF) - many fused rings (incl. a 8-member rings)
- BPA (e.g. 1JDG) - many fused rings
- CLR (e.g. 3GKI) - four fused rings
- Assembly symmetries
- 5M30 (Assembly 1, C3 local and pseudo)
- 1RB8 (Assembly 1, I global)