6CTX
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dCTP analogue
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0001701 | biological_process | in utero embryonic development |
A | 0003677 | molecular_function | DNA binding |
A | 0003684 | molecular_function | damaged DNA binding |
A | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
A | 0003906 | molecular_function | DNA-(apurinic or apyrimidinic site) endonuclease activity |
A | 0005515 | molecular_function | protein binding |
A | 0005634 | cellular_component | nucleus |
A | 0005654 | cellular_component | nucleoplasm |
A | 0005737 | cellular_component | cytoplasm |
A | 0005874 | cellular_component | microtubule |
A | 0005876 | cellular_component | spindle microtubule |
A | 0006259 | biological_process | DNA metabolic process |
A | 0006260 | biological_process | DNA replication |
A | 0006261 | biological_process | DNA-templated DNA replication |
A | 0006281 | biological_process | DNA repair |
A | 0006284 | biological_process | base-excision repair |
A | 0006287 | biological_process | base-excision repair, gap-filling |
A | 0006290 | biological_process | pyrimidine dimer repair |
A | 0006297 | biological_process | nucleotide-excision repair, DNA gap filling |
A | 0006303 | biological_process | double-strand break repair via nonhomologous end joining |
A | 0006915 | biological_process | apoptotic process |
A | 0006954 | biological_process | inflammatory response |
A | 0006974 | biological_process | DNA damage response |
A | 0007435 | biological_process | salivary gland morphogenesis |
A | 0008017 | molecular_function | microtubule binding |
A | 0008630 | biological_process | intrinsic apoptotic signaling pathway in response to DNA damage |
A | 0010332 | biological_process | response to gamma radiation |
A | 0016445 | biological_process | somatic diversification of immunoglobulins |
A | 0016446 | biological_process | somatic hypermutation of immunoglobulin genes |
A | 0016779 | molecular_function | nucleotidyltransferase activity |
A | 0016829 | molecular_function | lyase activity |
A | 0019899 | molecular_function | enzyme binding |
A | 0032991 | cellular_component | protein-containing complex |
A | 0034061 | molecular_function | DNA polymerase activity |
A | 0045471 | biological_process | response to ethanol |
A | 0046872 | molecular_function | metal ion binding |
A | 0048535 | biological_process | lymph node development |
A | 0048536 | biological_process | spleen development |
A | 0048872 | biological_process | homeostasis of number of cells |
A | 0051402 | biological_process | neuron apoptotic process |
A | 0051575 | molecular_function | 5'-deoxyribose-5-phosphate lyase activity |
A | 0055093 | biological_process | response to hyperoxia |
A | 0071707 | biological_process | immunoglobulin heavy chain V-D-J recombination |
A | 0071897 | biological_process | DNA biosynthetic process |
A | 0140078 | molecular_function | class I DNA-(apurinic or apyrimidinic site) endonuclease activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | binding site for residue MG T 101 |
Chain | Residue |
A | HOH587 |
A | HOH826 |
T | HOH231 |
T | HOH241 |
T | HOH251 |
site_id | AC2 |
Number of Residues | 6 |
Details | binding site for residue NA P 101 |
Chain | Residue |
P | DG9 |
P | HOH203 |
A | THR101 |
A | VAL103 |
A | ILE106 |
A | HOH789 |
site_id | AC3 |
Number of Residues | 6 |
Details | binding site for residue NA D 101 |
Chain | Residue |
A | LYS60 |
A | LEU62 |
A | VAL65 |
A | HOH742 |
D | DC3 |
D | HOH204 |
site_id | AC4 |
Number of Residues | 6 |
Details | binding site for residue NA A 401 |
Chain | Residue |
A | ASP190 |
A | ASP192 |
A | ASP256 |
A | MG402 |
A | VC9404 |
P | HOH206 |
site_id | AC5 |
Number of Residues | 5 |
Details | binding site for residue MG A 402 |
Chain | Residue |
A | ASP190 |
A | ASP192 |
A | NA401 |
A | VC9404 |
A | HOH526 |
site_id | AC6 |
Number of Residues | 3 |
Details | binding site for residue CL A 403 |
Chain | Residue |
A | ASN294 |
A | THR297 |
A | HOH804 |
site_id | AC7 |
Number of Residues | 25 |
Details | binding site for residue VC9 A 404 |
Chain | Residue |
A | GLY179 |
A | SER180 |
A | ARG183 |
A | SER188 |
A | GLY189 |
A | ASP190 |
A | ASP192 |
A | TYR271 |
A | PHE272 |
A | THR273 |
A | GLY274 |
A | ASP276 |
A | ASN279 |
A | NA401 |
A | MG402 |
A | HOH505 |
A | HOH509 |
A | HOH676 |
A | HOH688 |
A | HOH726 |
A | HOH741 |
P | 2DA10 |
P | HOH206 |
P | HOH208 |
T | DG6 |
site_id | AC8 |
Number of Residues | 10 |
Details | binding site for residue DC A 405 |
Chain | Residue |
A | ILE174 |
A | THR176 |
A | THR196 |
A | LYS262 |
A | TYR265 |
A | TYR266 |
A | HOH504 |
A | HOH525 |
A | HOH586 |
A | HOH593 |
Functional Information from PROSITE/UniProt
site_id | PS00522 |
Number of Residues | 20 |
Details | DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP |
Chain | Residue | Details |
A | GLY179-PRO198 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 1 |
Details | ACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863 |
Chain | Residue | Details |
A | LYS72 |
site_id | SWS_FT_FI2 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ |
Chain | Residue | Details |
A | LYS60 | |
A | LEU62 | |
A | VAL65 | |
A | THR101 | |
A | VAL103 | |
A | ILE106 |
site_id | SWS_FT_FI3 |
Number of Residues | 3 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY |
Chain | Residue | Details |
A | ARG149 | |
A | SER180 | |
A | GLY189 |
site_id | SWS_FT_FI4 |
Number of Residues | 1 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX |
Chain | Residue | Details |
A | ARG183 |
site_id | SWS_FT_FI5 |
Number of Residues | 3 |
Details | BINDING: BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY |
Chain | Residue | Details |
A | ASP190 | |
A | ASP192 | |
A | ASP256 |
site_id | SWS_FT_FI6 |
Number of Residues | 1 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409 |
Chain | Residue | Details |
A | LYS72 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | MOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869 |
Chain | Residue | Details |
A | ARG83 | |
A | ARG152 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556 |
Chain | Residue | Details |
A | LYS41 | |
A | LYS61 | |
A | LYS81 |