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 | 0005657 | cellular_component | replication fork |
| 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 | 0016787 | molecular_function | hydrolase activity |
| B | 0016829 | molecular_function | lyase activity |
| B | 0036297 | biological_process | interstrand cross-link repair |
| B | 0097681 | biological_process | double-strand break repair via alternative nonhomologous end joining |
| B | 0106300 | biological_process | protein-DNA covalent cross-linking repair |
| B | 0140431 | molecular_function | DNA-(abasic site) binding |
| 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 | Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"31235915","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31504793","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | Active site: {"evidences":[{"source":"PubMed","id":"35934051","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"37519246","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | Site: {"description":"Required for sensing abasic sites","evidences":[{"source":"PubMed","id":"31504793","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Site: {"description":"Required to stabilize abasic sites","evidences":[{"source":"PubMed","id":"31235915","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Thiazolidine linkage to a ring-opened DNA abasic site","evidences":[{"source":"PubMed","id":"31235915","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31504793","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
