Table 2. Examples of proteins with a predicted carboxylated lysine residue (pKcx).
The following are given: the PDB code and chain where the pKcx is predicted (PDB_chain), the residue number of the pKcx, the resolution of the protein structure in Å (RES) and the percentage similarity to any protein known to have a Kcx residue (SIM), where ‘Fg’ indicates that the similarity is detected in a fragment of a known KCX protein and ‘No’ indicates that no sequence similarity is detected.
| PDB_chain | pKcx | RES | SIM | Protein name | Source |
|---|---|---|---|---|---|
| 2jc7_A | 84 | 2.50 | 100 | Carbapenemase OXA-24 | Acinetobacter baumannii |
| 3msr_A | 153 | 2.16 | 100 | Amidohydrolase | Mycoplasma synoviae |
| 3feq_A | 188 | 2.63 | 98 | Amidohydrolase Sgx9260c | Unknown |
| 1iwa_A | 201 | 2.60 | 97 | RuBisCo | Galdieria partita |
| 3igh_X | 278 | 1.95 | 70 | Uncharacterized metal-dependent hydrolase | Pyrococcus horikoshii |
| 2vr2_A | 159 | 2.80 | 60 | Human dihydropyrimidinase | Homo sapiens |
| 3hm7_A | 150 | 2.60 | 40 | Allantoinase | Bacillus halodurans |
| 2cwx_A | 186 | 2.00 | 40 | RuBisCo | Pyrococcus horikoshii |
| 2qs8_A | 194 | 2.33 | 36 | Dipeptidase | Alteromonas macleodii |
| 2gok_A | 155 | 1.87 | 30 | Imidazolonepropionase | Agrobacterium tumefaciens |
| 2bb0_A | 149 | 2.00 | 30 | Imidazolonepropionase | Bacillus subtilis |
| 2oof_A | 141 | 2.20 | 30 | Imidazolonepropionase | Environmental sample |
| 4fr4_A | 184 | 2.29 | 26 | Serine/threonine protein kinase | Homo sapiens |
| 1ckj_A | 237 | 2.46 | 24 | Casein kinase 1δ | Rattus norvegicus |
| 1iyx_A | 390 | 2.80 | 23 | Enolase | Enterococcus hirae |
| 2p2s_A | 96 | 1.25 | Fg | Putative oxidoreductase | Erwinia carotovora atroseptica |
| 3c4u_A | 251 | 1.83 | Fg | Class II fructose-bisphosphate aldolase | Helicobacter pylori |
| 2jc7_D | 205 | 2.00 | Fg | Glucarate dehydratase | Escherichia coli |
| 4g9p_A | 204 | 1.55 | Fg | GcpE (IspG)–MEcPP | Thermus thermophilus |
| 1f3o_A | 44 | 2.70 | Fg | MJ0796 ATP-binding cassette | Methanocaldococcus jannaschii |
| 2fiq_A | 279 | 2.25 | No | Putative tagatose 6-phosphate kinase | Escherichia coli |
| 1qwr_A | 96 | 1.80 | No | Mannose 6-phosphate isomerase | Bacillus subtilis |
| 3tcs_A | 145 | 1.88 | No | Putative racemase | Roseobacter denitrificans |
| 3u4f_A | 145 | 1.90 | No | Mandelate racemase | Roseovarius nubinhibens |
| 3uhj_A | 298 | 2.34 | No | Glycerol dehydrogenase | Sinorhizobium meliloti |
| 1xe7_A | 147 | 1.75 | No | Yml079w | Saccharomyces cerevisiae |
| 1mdo_A | 188 | 1.70 | No | Aminotransferase | Salmonella typhimurium |
| 2as9_A | 32 | 1.70 | No | Serine protease | Staphylococcus aureus |
| 2eb0_B | 294 | 2.20 | No | Mn-dependent inorganic pyrophosphatase | Methanocaldococcus jannaschii |
| 2ejc_A | 149 | 2.40 | No | Pantoate-β-alanine ligase | Thermotoga maritima |
| 2huo_A | 127 | 2.00 | No | Inositol oxygenase | Mus musculus |
| 2ptx_A | 343 | 1.90 | No | Enolase | Trypanosoma brucei |
| 2w8s_B | 337 | 2.40 | No | Phosphonate monoester hydrolase | Burkholderia caryophylli |
| 3igy_B | 357 | 2.00 | No | Phosphoglycerate mutase | Leishmania mexicana |