Structure of PDB 8udk Chain A Binding Site BS03

Receptor Information

>8udk Chain A (length=1012) Species: 9606 (Homo sapiens)

QLRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPA
VPLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPP
AWAWAEGWTRYGPEGEAVPVAIPEERALVFAVAVCLAEGTCPTLAVAISP
SAWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTQEQLVVGHNVSFDRAH
IREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGISSWDWLDI
SSVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDV
WATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQG
TYEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKDQ
EDLGPCSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLC
PRLDDPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVVCP
YRAIESLYRKHCLEQARGGPKDTQPSYHHGNGPYNDVDIPGCWFFKLPHK
DGNSCNVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAH
KRISSQMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRAAV
EPTWLTASNARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDA
HFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIY
GAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLSDWLVREL
NLPVDRTEGGWISLQDLRKERAWKGGTESEMFNKLESIATSDIPRTPVLG
CCISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAID
GRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQS
VAFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIEL
TKGSLEKRSQPG

Ligand information

• Ligand ID: DCP
• InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: RGWHQCVHVJXOKC-SHYZEUOFSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
• Formula: C9 H16 N3 O13 P3
• Name: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL560403
• DrugBank: DB03258
• ZINC: ZINC000008215945
• PDB chain: 8udk Chain A Residue 4000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8udk An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol gamma.
• Resolution: 3.43 Å
• Binding residue (original residue number in PDB): D890 S893 R943 E1192
• Binding residue (residue number reindexed from 1): D685 S688 R738 E966
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.-
  4.2.99.-

Gene Ontology

Molecular Function

• GO:0002020 protease binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0016787 hydrolase activity
• GO:0016829 lyase activity
• GO:0051575 5'-deoxyribose-5-phosphate lyase activity

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006264 mitochondrial DNA replication
• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006287 base-excision repair, gap-filling
• GO:0045004 DNA replication proofreading
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0000262 mitochondrial chromosome
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0005760 gamma DNA polymerase complex
• GO:0032991 protein-containing complex
• GO:0042645 mitochondrial nucleoid
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:8udk, PDBe:8udk, PDBj:8udk
• PDBsum: 8udk
• PubMed: 38787958
• UniProt: P54098|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)