Structure of PDB 3au6 Chain A Binding Site BS02

Receptor Information
>3au6 Chain A (length=562) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEK
GKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPG
VGPKTARLLYEGLGIDSLEKLKAALDRGFGPKRAERIREGLALAQAAGKR
RPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASRE
GERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQ
YLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLP
WIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEEL
WEAAKTMGYRYLAVTDHSPAVRVGPSPEEALKRVGEIRRFNETHGPPYLL
AGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALE
NPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDL
PDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNT
LDYEDLLSWLKA
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 chain3au6 Chain A Residue 576 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3au6 The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		R157 G187 S188 R191 V196 G197 D198 D200 Y258 K263 R270
Binding residue
(residue number reindexed from 1)		R150 G180 S181 R184 V189 G190 D191 D193 Y251 K256 R263
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.92,Kd=12nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3au6, PDBe:3au6, PDBj:3au6
PDBsum3au6
PubMed22306405
UniProtQ5SJ64

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