Structure of PDB 1huo Chain A Binding Site BS04

Receptor Information

>1huo Chain A (length=325) Species: 10116 (Rattus norvegicus)

TLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPS
AARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQ
DIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPK
LLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENDENEYPHRRIDIRL
IPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGE
PLPVDSEQDIFDYIQWRYREPKDRS

Ligand information

• Ligand ID: TTE
• InChI: InChI=1S/C11H19N2O13P3/c1-6-3-13(11(16)12-10(6)15)9-2-7(14)8(25-9)4-24-29(22,23)26-28(20,21)5-27(17,18)19/h3,7-9,14H,2,4-5H2,1H3,(H,20,21)(H,22,23)(H,12,15,16)(H2,17,18,19)/t7-,8+,9+/m0/s1
• InChIKey: HEDAITKJNKXWIZ-DJLDLDEBSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(CP(=O)(O)O)O)O
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)C[P](O)(O)=O)O2)C(=O)NC1=O
• Formula: C11 H19 N2 O13 P3
• Name: PHOSPHOMETHYL PHOSPHONIC ACID DEOXYTHYMIDYLATE ESTER
• ZINC: ZINC000013531971
• PDB chain: 1huo Chain A Residue 338

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1huo Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): G179 S180 R183 S188 G189 D190 D192 Y271 F272 D276
• Binding residue (residue number reindexed from 1): G170 S171 R174 S179 G180 D181 D183 Y262 F263 D267
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D190 D192 D256
• Catalytic site (residue number reindexed from 1): D181 D183 D247
• 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:1huo, PDBe:1huo, PDBj:1huo
• PDBsum: 1huo
• PubMed: 11330999
• UniProt: P06766|DPOLB_RAT DNA polymerase beta (Gene Name=Polb)