6KIJ
Crystal structure of yedK with ssDNA containing an abasic site
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003697 | molecular_function | single-stranded DNA binding |
| B | 0006508 | biological_process | proteolysis |
| B | 0006974 | biological_process | DNA damage response |
| B | 0008233 | molecular_function | peptidase activity |
| B | 0009432 | biological_process | SOS response |
| B | 0016829 | molecular_function | lyase activity |
| B | 0106300 | biological_process | protein-DNA covalent cross-linking repair |
| B | 0160129 | molecular_function | protein-DNA covalent cross-linking activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | binding site for residue PED B 301 |
| Chain | Residue |
| A | DC1 |
| B | HOH517 |
| B | HOH534 |
| B | CYS2 |
| B | GLY3 |
| B | ASN75 |
| B | ARG77 |
| B | THR149 |
| B | HIS160 |
| B | ARG162 |
| B | HOH462 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue GOL B 302 |
| Chain | Residue |
| B | ASP21 |
| B | TYR28 |
| B | HOH602 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:31235915, ECO:0000269|PubMed:31504793 |
| Chain | Residue | Details |
| B | CYS2 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | ACT_SITE: ACT_SITE => ECO:0000305|PubMed:35934051, ECO:0000305|PubMed:37519246 |
| Chain | Residue | Details |
| B | GLU105 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | SITE: Required for sensing abasic sites => ECO:0000269|PubMed:31504793 |
| Chain | Residue | Details |
| B | GLU105 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | SITE: Required to stabilize abasic sites => ECO:0000269|PubMed:31235915 |
| Chain | Residue | Details |
| B | HIS160 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | MOD_RES: Thiazolidine linkage to a ring-opened DNA abasic site => ECO:0000269|PubMed:31235915, ECO:0000269|PubMed:31504793 |
| Chain | Residue | Details |
| B | CYS2 |
