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 |