Structure of PDB 3t3f Chain A Binding Site BS05

Receptor Information
>3t3f Chain A (length=533) 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
ASWMVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQS
FPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAF
NMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAV
ARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
Ligand information
Ligand IDN5P
InChIInChI=1S/C13H17N2O14P3/c16-11-6-13(14-4-3-8-5-9(15(17)18)1-2-10(8)14)27-12(11)7-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-5,11-13,16H,6-7H2,(H,22,23)(H,24,25)(H2,19,20,21)/t11-,12+,13+/m0/s1
InChIKeyJJJBDAFRCKSXDR-YNEHKIRRSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
OpenEye OEToolkits 1.7.2c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
ACDLabs 12.01[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
FormulaC13 H17 N2 O14 P3
Name1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE;
5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000059142887
PDB chain3t3f Chain A Residue 836 [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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PDB3t3f Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D610 Y611 Q613 I614 E615 H639 R659 K663 F667 D785
Binding residue
(residue number reindexed from 1)		D318 Y319 Q321 I322 E323 H347 R360 K364 F368 D486
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:3t3f, PDBe:3t3f, PDBj:3t3f
PDBsum3t3f
PubMed22318723
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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