Interesting Structures
From Proteopedia
(Difference between revisions)
(New page: Pages from [https://raw.githubusercontent.com/molstar/molstar/master/docs/interesting-pdb-entries.md] * Cyclic polymers (1sfi, 6dny, 1HVZ) * B-DNA (1bna) * Missing carbonyl oxygen (1gfl) ...) |
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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 [https://raw.githubusercontent.com/molstar/molstar/master/docs/interesting-pdb-entries.md] | ||
| - | * Cyclic polymers (1sfi, 6dny, | + | * Cyclic polymers ([[1sfi]], [[6dny]], [[1hvz]]) |
| - | * B-DNA (1bna) | + | * B-DNA ([[1bna]]) |
| - | * Missing carbonyl oxygen (1gfl) | + | * Missing carbonyl oxygen ([[1gfl]]) |
| - | * Mono-saccharides with alt locs ( | + | * Mono-saccharides with alt locs ([[1b5f]]) |
* Microheterogeneity | * Microheterogeneity | ||
| - | + | : Protein ([[1ejg]], [[3nir]]) | |
| - | + | : DNA ([[3vok]]) | |
* PNA: peptide nucleic acid ([[5eme]], [[1xj9]]) | * PNA: peptide nucleic acid ([[5eme]], [[1xj9]]) | ||
* Peptide derived residues | * Peptide derived residues | ||
| - | + | : GFP chromophores ([[5z6y]]) | |
| - | * Nucleotides that don’t have a parent base set, i.e. detect purine/pyrimidine from geometry (THX in | + | * 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 | * 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. | + | * Beta & Gamma peptides (e.g. [[1gac]], [[6pqf]]) |
| - | * Mixed (heterogeneous) all-atom/trace-only RNA model ( | + | * Mixed (heterogeneous) all-atom/trace-only RNA model ([[1jgq]]) |
| - | * Polymers with residues with missing trace atoms (e.g. | + | * Polymers with residues with missing trace atoms (e.g. [[2qfj]]) |
| - | * Modified RNA bases (1y26, | + | * Modified RNA bases ([[1y26]], [[5l4o]]) |
| - | * Discontinuous chains, i.e. gaps in the sequence (3sn6) | + | * Discontinuous chains, i.e. gaps in the sequence ([[3sn6]]) |
* Lots of sheets ([[1cbs]]) | * Lots of sheets ([[1cbs]]) | ||
* DNA ([[2np2]], [[1d66]]) | * DNA ([[2np2]], [[1d66]]) | ||
* C-alpha only ([[2rcj]]) | * C-alpha only ([[2rcj]]) | ||
| - | * Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible ( | + | * 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]]) | * Close backbone atoms but not linked (e.g. [[4hiv]]) | ||
* Non-standard residues | * Non-standard residues | ||
| - | + | : Protein ([[1brr]], [[5z6y]]) | |
| - | + | : DNA ([[5d3g]]) | |
| - | * Multiple models with different sets of ligands or missing ligands ( | + | * Multiple models with different sets of ligands or missing ligands ([[1j6t]], [[1vrc]], [[2icy]], [[1o2f]]) |
Current revision
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
- 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
- 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
