Structure of PDB 3auo Chain B Binding Site BS02

Receptor Information
>3auo Chain B (length=572) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEK
GKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPG
VGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLAL
AQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLD
FLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPE
SYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEV
YAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDG
QNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFN
ETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQ
TKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEI
DGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAW
IGPERVLNTLDYEDLLSWLKAR
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 chain3auo Chain B Residue 576 [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]
PDB3auo The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		R157 S188 R191 V196 G197 D198 D200 Y258 L259 K263 R270
Binding residue
(residue number reindexed from 1)		R157 S188 R191 V196 G197 D198 D200 Y258 L259 K263 R270
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003824 catalytic activity
GO:0003887 DNA-directed DNA polymerase activity
GO:0008270 zinc ion binding
GO:0042578 phosphoric ester hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0071897 DNA biosynthetic process
GO:0071978 bacterial-type flagellum-dependent swarming motility
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3auo, PDBe:3auo, PDBj:3auo
PDBsum3auo
PubMed22306405
UniProtQ5SJ64

[Back to BioLiP]