Structure of PDB 3uxp Chain B Binding Site BS03

Receptor Information

>3uxp Chain B (length=326) Species: 10116 (Rattus norvegicus)

ETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAE
AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGP
SAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQM
QDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQP
KLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENDENEYPHRRIDIR
LQPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAG
EPLPVDSEQDIFDYIQWRYREPKDRS

Ligand information

• Ligand ID: D3T
• InChI: InChI=1S/C10H17N2O13P3/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(23-8)5-22-27(18,19)25-28(20,21)24-26(15,16)17/h4,7-8H,2-3,5H2,1H3,(H,18,19)(H,20,21)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1
• InChIKey: URGJWIFLBWJRMF-JGVFFNPUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CCC(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
  CACTVS 3.341: CC1=CN([C@H]2CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
  CACTVS 3.341: CC1=CN([CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
• Formula: C10 H17 N2 O13 P3
• Name: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL566812
• ZINC: ZINC000013519271
• PDB chain: 3uxp Chain B Residue 336

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3uxp Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta.
• Resolution: 2.723 Å
• Binding residue (original residue number in PDB): R149 G179 S180 S188 D192 Y271
• Binding residue (residue number reindexed from 1): R141 G171 S172 S180 D184 Y263
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D190 D192 D256
• Catalytic site (residue number reindexed from 1): D182 D184 D248
• 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:3uxp, PDBe:3uxp, PDBj:3uxp
• PDBsum: 3uxp
• PubMed: 23651085
• UniProt: P06766|DPOLB_RAT DNA polymerase beta (Gene Name=Polb)