6KBZ
Crystal structure of yedK with ssDNA containing a tetrahydrofuran 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 |
| D | 0003677 | molecular_function | DNA binding |
| D | 0003697 | molecular_function | single-stranded DNA binding |
| D | 0006508 | biological_process | proteolysis |
| D | 0006974 | biological_process | DNA damage response |
| D | 0008233 | molecular_function | peptidase activity |
| D | 0009432 | biological_process | SOS response |
| D | 0016829 | molecular_function | lyase activity |
| D | 0106300 | biological_process | protein-DNA covalent cross-linking repair |
| D | 0160129 | molecular_function | protein-DNA covalent cross-linking activity |
| F | 0003677 | molecular_function | DNA binding |
| F | 0003697 | molecular_function | single-stranded DNA binding |
| F | 0006508 | biological_process | proteolysis |
| F | 0006974 | biological_process | DNA damage response |
| F | 0008233 | molecular_function | peptidase activity |
| F | 0009432 | biological_process | SOS response |
| F | 0016829 | molecular_function | lyase activity |
| F | 0106300 | biological_process | protein-DNA covalent cross-linking repair |
| F | 0160129 | molecular_function | protein-DNA covalent cross-linking activity |
| H | 0003677 | molecular_function | DNA binding |
| H | 0003697 | molecular_function | single-stranded DNA binding |
| H | 0006508 | biological_process | proteolysis |
| H | 0006974 | biological_process | DNA damage response |
| H | 0008233 | molecular_function | peptidase activity |
| H | 0009432 | biological_process | SOS response |
| H | 0016829 | molecular_function | lyase activity |
| H | 0106300 | biological_process | protein-DNA covalent cross-linking repair |
| H | 0160129 | molecular_function | protein-DNA covalent cross-linking activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 301 |
| Chain | Residue |
| B | ASP140 |
| B | HOH432 |
| B | HOH436 |
| B | HOH514 |
| B | HOH518 |
| B | HOH581 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 302 |
| Chain | Residue |
| F | MG301 |
| F | HOH415 |
| B | ASP111 |
| B | HOH462 |
| B | HOH475 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue MG F 301 |
| Chain | Residue |
| B | MG302 |
| B | HOH462 |
| F | ASP140 |
| F | HOH415 |
| F | HOH443 |
| F | HOH496 |
| F | HOH571 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue MG H 301 |
| Chain | Residue |
| D | ASP111 |
| D | HOH303 |
| D | HOH390 |
| H | ASP140 |
| H | HOH491 |
| H | HOH517 |
| H | HOH557 |
| site_id | AC5 |
| Number of Residues | 16 |
| Details | binding site for Di-nucleotide DT C 1 and 3DR C 2 |
| Chain | Residue |
| C | DG0 |
| C | DG3 |
| C | HOH104 |
| C | HOH107 |
| C | HOH124 |
| C | HOH128 |
| D | CYS2 |
| D | GLY3 |
| D | ASN75 |
| D | ARG77 |
| D | PHE87 |
| D | THR149 |
| D | ARG162 |
| G | DG0 |
| G | DT1 |
| G | HOH107 |
| site_id | AC6 |
| Number of Residues | 19 |
| Details | binding site for Di-nucleotide 3DR C 2 and DG C 3 |
| Chain | Residue |
| C | DT1 |
| C | DA4 |
| C | HOH108 |
| C | HOH110 |
| C | HOH123 |
| C | HOH124 |
| C | HOH128 |
| C | HOH129 |
| D | CYS2 |
| D | GLY3 |
| D | ARG4 |
| D | PRO40 |
| D | ASN75 |
| D | ARG77 |
| D | THR149 |
| D | ARG162 |
| D | VAL211 |
| G | DC7 |
| H | PRO71 |
| site_id | AC7 |
| Number of Residues | 16 |
| Details | binding site for Di-nucleotide DT E 1 and 3DR E 2 |
| Chain | Residue |
| A | DG0 |
| A | DT1 |
| E | DG0 |
| E | DG3 |
| E | HOH117 |
| E | HOH123 |
| F | CYS2 |
| F | GLY3 |
| F | ASN75 |
| F | ARG77 |
| F | PHE87 |
| F | THR149 |
| F | HIS160 |
| F | ARG162 |
| F | HOH418 |
| F | HOH436 |
| site_id | AC8 |
| Number of Residues | 21 |
| Details | binding site for Di-nucleotide 3DR E 2 and DG E 3 |
| Chain | Residue |
| A | DC7 |
| B | PRO71 |
| E | DT1 |
| E | DA4 |
| E | HOH103 |
| E | HOH104 |
| E | HOH111 |
| E | HOH123 |
| E | HOH124 |
| E | HOH125 |
| E | HOH126 |
| F | CYS2 |
| F | GLY3 |
| F | ARG4 |
| F | PRO40 |
| F | ASN75 |
| F | ARG77 |
| F | THR149 |
| F | HIS160 |
| F | ARG162 |
| F | VAL211 |
| site_id | AC9 |
| Number of Residues | 18 |
| Details | binding site for Di-nucleotide DT G 1 and 3DR G 2 |
| Chain | Residue |
| G | DG0 |
| G | DG3 |
| G | HOH103 |
| G | HOH107 |
| G | HOH108 |
| G | HOH113 |
| G | HOH124 |
| G | HOH127 |
| G | HOH135 |
| H | CYS2 |
| H | GLY3 |
| H | ASN75 |
| H | ARG77 |
| H | PHE87 |
| H | THR149 |
| H | ARG162 |
| C | DG0 |
| C | DT1 |
| site_id | AD1 |
| Number of Residues | 20 |
| Details | binding site for Di-nucleotide 3DR G 2 and DG G 3 |
| Chain | Residue |
| C | DC7 |
| D | HOH359 |
| G | DT1 |
| G | DA4 |
| G | HOH108 |
| G | HOH111 |
| G | HOH114 |
| G | HOH124 |
| G | HOH127 |
| G | HOH128 |
| G | HOH133 |
| H | CYS2 |
| H | GLY3 |
| H | ARG4 |
| H | PRO40 |
| H | ASN75 |
| H | ARG77 |
| H | THR149 |
| H | ARG162 |
| H | VAL211 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:31235915, ECO:0000269|PubMed:31504793 |
| Chain | Residue | Details |
| B | CYS2 | |
| D | CYS2 | |
| F | CYS2 | |
| H | CYS2 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: ACT_SITE => ECO:0000305|PubMed:35934051, ECO:0000305|PubMed:37519246 |
| Chain | Residue | Details |
| B | GLU105 | |
| D | GLU105 | |
| F | GLU105 | |
| H | GLU105 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | SITE: Required for sensing abasic sites => ECO:0000269|PubMed:31504793 |
| Chain | Residue | Details |
| B | GLU105 | |
| D | GLU105 | |
| F | GLU105 | |
| H | GLU105 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | SITE: Required to stabilize abasic sites => ECO:0000269|PubMed:31235915 |
| Chain | Residue | Details |
| B | HIS160 | |
| D | HIS160 | |
| F | HIS160 | |
| H | HIS160 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| 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 | |
| D | CYS2 | |
| F | CYS2 | |
| H | CYS2 |
