Structure of PDB 3rr8 Chain A Binding Site BS03

Receptor Information
>3rr8 Chain A (length=534) Species: 271 (Thermus aquaticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKAL
RDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVAR
RYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLA
HMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLER
VLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK
STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQ
RIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTET
ASWMFGVPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQ
SFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMA
FNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEA
VARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
Ligand information
Ligand IDDG3
InChIInChI=1S/C10H16N5O12P3/c11-10-13-8-7(9(16)14-10)12-4-15(8)6-2-1-5(25-6)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h4-6H,1-3H2,(H,20,21)(H,22,23)(H2,17,18,19)(H3,11,13,14,16)/t5-,6+/m0/s1
InChIKeyHDRRAMINWIWTNU-NTSWFWBYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CCC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O12 P3
Name2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL54224
DrugBank
ZINCZINC000013516810
PDB chain3rr8 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3rr8 Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R587 Q613 R659 K663 F667 Y671
Binding residue
(residue number reindexed from 1)		R295 Q321 R361 K365 F369 Y373
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0001882 nucleoside binding
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
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3rr8, PDBe:3rr8, PDBj:3rr8
PDBsum3rr8
PubMed22318723
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

[Back to BioLiP]