This directory contains example entries which are affected by the remediation and the CCD files that describe the protein modifications in these entries.
For comparison, the original and updated files are provided for all these files.
The table below gives an overview of these files.
| PDB ID | Protein modifications present |
|---|---|
| 1SZA | 1 Phosphoserine |
| 4ZPZ | 2 Phosphoserines and 1 disulfide bridge |
| 1J04 | 1 Pyridoxal phosphate attached to lysine |
| 5YY9 | 2 Trimethyl lysines |
| 2K4H | 1 Myristic acid covalently bonded to glycine |
| 6J6M | 1 Covalent chemical modification (Zanubrutinib) |
| 7C7P | 2 Covalent chemical modifications (Telaprevir) |
| 2THF | 1 Covalent chemical modification linked to 2 residues and 4 disulfide bridges |
| 2CFH | 2 Palmitic acids covalently bonded to lysines and 2 hydroxy-cysteines |
| 1B7V | 1 Heme C covalently bonded to two cysteines |
| 1HUY | 1 Chromophore |
| 1FFM | 1 Carbohydrate covalently bonded to serine and 4 disulfide bridges |
| 1AC5 | 2 Carbohydrates covalently bonded to asparagine and 3 disulfide bridges |
| 1I86 | 1 Modified residue containing two types of modification (cysteinesulfinic acid) |
| 1B30 | 1 Pyrrolidone carboxylic acid |
| 1A93 | 2 Proteins with capped with acetylation and amidation (ACE and NH2) and 1 disulfide bridge |
| 1M72 | 1 Chloromethylketone peptide covalent inhibitor |
| 6Y5D | 9 Pentanedial crosslinkers that covalently bond to lysines |
| 2XSK | 1 Non-standard linkage (between two selenocysteines) and a selenomethionine |
| 3DVN | 2 Isopeptide bonds and 8 disulfide bridges |
| 1DIN | Microheterogeniety where cysteinesulfinic acid is the main occupancy and cysteine is the secondary occupancy |
| 5VF5 | Microheterogeniety where cysteine is the main occupancy and cysteinesulfinic acid is the secondary occupancy |
| 7AZ5 | 4 Synthetic peptides with non-standard residues and N-terminal acetylations |
| CCD ID | Description |
|---|---|
| SEP | Phosphoserine |
| LLP | N6-(pyridoxal phosphate)-lysine |
| M3L | N6,N6,N6-Trimethyl-lysine |
| MYR | Myristic acid |
| BA0 | Zanubrutinib |
| SV6 | Telaprevir |
| 0G6 | Chloromethylketone inhibitor |
| PLM | Palmitic acid |
| CSO | S-Hydroxycysteine |
| HEC | Heme C |
| CRO | Peptide derived chromophore |
| FUC | Alpha-L-fucopyranose |
| NAG | N-Acetyl-D-Glucosamine |
| CSD | 3-Sulfinoalanine |
| PCA | Pyrrolidone carboxylic acid |
| ACE | N-terminal acetyl group |
| NH2 | C-terminal amino group |
| 0QE | Chloromethane |
| PTD | Pentanedial |
| MSE | Selenomethionine |
| ALC | Non-standard residue |
| OIC | Non-standard residue |