5TB8
Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)3TC-TP and Mn2+.
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 | 21 |
| Details | binding site for residue 1RZ A 401 |
| Chain | Residue |
| A | GLY179 |
| A | ASP276 |
| A | ASN279 |
| A | MN405 |
| A | MN406 |
| A | HOH513 |
| A | HOH514 |
| A | HOH530 |
| A | HOH537 |
| A | HOH557 |
| A | HOH600 |
| A | SER180 |
| P | DC10 |
| T | DG6 |
| A | ARG183 |
| A | SER188 |
| A | GLY189 |
| A | ASP190 |
| A | ASP192 |
| A | TYR271 |
| A | PHE272 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue MN A 402 |
| Chain | Residue |
| A | HIS337 |
| A | HIS339 |
| A | HOH511 |
| A | HOH647 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue MN A 403 |
| Chain | Residue |
| A | GLU117 |
| A | ASP321 |
| A | ACT417 |
| A | HOH535 |
| A | HOH624 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue MN A 404 |
| Chain | Residue |
| A | LYS48 |
| A | HIS336 |
| A | HIS338 |
| A | HOH592 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue MN A 405 |
| Chain | Residue |
| A | ASP190 |
| A | ASP192 |
| A | 1RZ401 |
| A | MN406 |
| A | HOH530 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue MN A 406 |
| Chain | Residue |
| A | ASP190 |
| A | ASP192 |
| A | ASP256 |
| A | 1RZ401 |
| A | MN405 |
| A | HOH557 |
| A | HOH603 |
| P | DC10 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | binding site for residue MN A 407 |
| Chain | Residue |
| A | HIS285 |
| A | GLU288 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue NA A 408 |
| Chain | Residue |
| A | ASP130 |
| A | ASP314 |
| A | HOH520 |
| A | HOH564 |
| A | HOH644 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue NA A 409 |
| Chain | Residue |
| A | ASP145 |
| A | HIS252 |
| A | HOH590 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue NA A 410 |
| Chain | Residue |
| A | LYS60 |
| A | LEU62 |
| A | VAL65 |
| D | DC3 |
| D | HOH112 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 411 |
| Chain | Residue |
| A | THR101 |
| A | VAL103 |
| A | ILE106 |
| A | HOH650 |
| P | DG9 |
| P | HOH106 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 412 |
| Chain | Residue |
| A | ASP91 |
| A | GLN157 |
| A | ACT416 |
| A | HOH542 |
| A | HOH550 |
| A | HOH613 |
| site_id | AD4 |
| Number of Residues | 2 |
| Details | binding site for residue CL A 413 |
| Chain | Residue |
| A | ASN294 |
| A | THR297 |
| site_id | AD5 |
| Number of Residues | 3 |
| Details | binding site for residue CL A 414 |
| Chain | Residue |
| A | ALA32 |
| A | ILE33 |
| A | HIS34 |
| site_id | AD6 |
| Number of Residues | 8 |
| Details | binding site for residue ACT A 415 |
| Chain | Residue |
| A | HIS34 |
| A | ASN37 |
| A | ALA38 |
| A | LYS41 |
| A | LYS280 |
| A | HOH538 |
| D | DG1 |
| T | DC5 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue ACT A 416 |
| Chain | Residue |
| A | VAL29 |
| A | ASP91 |
| A | GLN157 |
| A | ASP160 |
| A | NA412 |
| A | HOH550 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue ACT A 417 |
| Chain | Residue |
| A | GLU117 |
| A | ASP321 |
| A | TYR322 |
| A | MN403 |
| site_id | AD9 |
| Number of Residues | 2 |
| Details | binding site for residue ACT A 418 |
| Chain | Residue |
| A | TYR36 |
| A | HOH504 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue ACT A 419 |
| Chain | Residue |
| A | LYS127 |
| A | HOH505 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue ACT A 420 |
| Chain | Residue |
| A | ASP246 |
| A | TRP325 |
| A | LYS326 |
| A | ARG328 |
| A | HOH570 |
| A | HOH653 |
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 |
