Structure of PDB 8efc Chain A Binding Site BS03

Receptor Information
>8efc Chain A (length=595) Species: 8187 (Lates calcarifer) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFSIIDVASDRRLFNTFIKEWKTKERYSLALACEKREHDSDGLVLIGLSV
CWGARDSYYISLQQVSERLGQVRSCLSRPGGVVVTYDIIQVYKTLVLSCG
ISLAGNCEDPKVACWLLDPGSEERTLPNMVTVYCPEELPLLDGLAHCPRV
RAATKSVLVHAVMNHLTGLLEKDSMLDLFRSIEMPSQVCLALLELNGVGF
SVEECERQKHVMQAKLTALESQAYNLAGHSFSLTSIDDIAQVLFLELHLP
QFSTTKDILEKLRPLHPLPGVILEWRRITNALTKVVFPLQREKQYHPTLA
MDRIYPIAQTHTATGRVSFTEPNIQNVPKDFEICMAFSVSMRHAFVPFSG
GMILAADYSQLELRVLAHLSKDQRLLQVLNGGADVFRCIAAEWKGVDPET
VNDSLRQQAKQICYGIIYGMGAKSLGEQMGVEENDAACYIESFKARYKGI
NAFLKETVKNCIKNGYVQTLMGRRRYLPGISNTNTHIKAHAERQAVNTTV
QGSAADIVKLATVNIQKRLRKTYPTAPLSHQHTLRGAFFVLQLHDELIYE
TREEDLIQVAQIVKREMESAVKLYVKLKAKVKVGPSWGNLQDLDL
Ligand information
Ligand IDDGT
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O13 P3
Name2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL477486
DrugBankDB02181
ZINCZINC000008215755
PDB chain8efc Chain A Residue 2801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8efc Structural basis of DNA polymerase theta mediated DNA end joining.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		R2382 Y2464 Q2466 E2468 R2512 K2516 Q2517 Y2520 Y2524 D2664
Binding residue
(residue number reindexed from 1)		R316 Y358 Q360 E362 R406 K410 Q411 Y414 Y418 D545
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8efc, PDBe:8efc, PDBj:8efc
PDBsum8efc
PubMed36583344
UniProtA0A4W6BKE5

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