Structure of PDB 2bpg Chain B Binding Site BS03

Receptor Information

>2bpg Chain B (length=324) Species: 10116 (Rattus norvegicus)

ETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAE
AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGP
SAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQM
QDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQP
KLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENEYPHRRIDIRLIP
KDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPL
PVDSEQDIFDYIQWRYREPKDRSE

Ligand information

• Ligand ID: DCT
• InChI: InChI=1S/C9H16N3O12P3/c10-7-3-4-12(9(13)11-7)8-2-1-6(22-8)5-21-26(17,18)24-27(19,20)23-25(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
• InChIKey: ARLKCWCREKRROD-POYBYMJQSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1CC(OC1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
  OpenEye OEToolkits 1.5.0: C1C[C@@H](O[C@@H]1CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2
• Formula: C9 H16 N3 O12 P3
• Name: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
• ChEMBL: CHEMBL1201384
• ZINC: ZINC000013516800
• PDB chain: 2bpg Chain B Residue 338

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2bpg Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): S180 S188 G189 D190 D192 Y271 D276
• Binding residue (residue number reindexed from 1): S172 S180 G181 D182 D184 Y260 D265
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D190 D192 D256
• Catalytic site (residue number reindexed from 1): D182 D184 D245
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  4.2.99.-
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008017 microtubule binding
• GO:0016779 nucleotidyltransferase activity
• GO:0016829 lyase activity
• GO:0019899 enzyme binding
• GO:0034061 DNA polymerase activity
• GO:0046872 metal ion binding
• GO:0051575 5'-deoxyribose-5-phosphate lyase activity
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0001701 in utero embryonic development
• GO:0006259 DNA metabolic process
• GO:0006260 DNA replication
• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006287 base-excision repair, gap-filling
• GO:0006290 pyrimidine dimer repair
• GO:0006297 nucleotide-excision repair, DNA gap filling
• GO:0006303 double-strand break repair via nonhomologous end joining
• GO:0006915 apoptotic process
• GO:0006954 inflammatory response
• GO:0006974 DNA damage response
• GO:0007435 salivary gland morphogenesis
• GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
• GO:0010332 response to gamma radiation
• GO:0016445 somatic diversification of immunoglobulins
• GO:0016446 somatic hypermutation of immunoglobulin genes
• GO:0045471 response to ethanol
• GO:0048535 lymph node development
• GO:0048536 spleen development
• GO:0048872 homeostasis of number of cells
• GO:0051402 neuron apoptotic process
• GO:0055093 response to hyperoxia
• GO:0071707 immunoglobulin heavy chain V-D-J recombination
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005874 microtubule
• GO:0005876 spindle microtubule
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:2bpg, PDBe:2bpg, PDBj:2bpg
• PDBsum: 2bpg
• PubMed: 7516580
• UniProt: P06766|DPOLB_RAT DNA polymerase beta (Gene Name=Polb)