Structure of PDB 1tkd Chain A Binding Site BS05

Receptor Information
>1tkd Chain A (length=698) Species: 10760 (Escherichia phage T7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEV
ARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHS
NLKDTDMGLLRSGKLPGALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVD
GMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTF
WSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRK
LTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQ
REGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKY
TDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAW
LRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFG
AEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIH
TKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFL
ENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSP
HAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEI
QVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
Ligand information
Ligand IDD3T
InChIInChI=1S/C10H17N2O13P3/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(23-8)5-22-27(18,19)25-28(20,21)24-26(15,16)17/h4,7-8H,2-3,5H2,1H3,(H,18,19)(H,20,21)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1
InChIKeyURGJWIFLBWJRMF-JGVFFNPUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CCC(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
CACTVS 3.341CC1=CN([C@H]2CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
CACTVS 3.341CC1=CN([CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O13 P3
Name2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL566812
DrugBank
ZINCZINC000013519271
PDB chain1tkd Chain A Residue 823 [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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PDB1tkd Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
Resolution2.49 Å
Binding residue
(original residue number in PDB)		R429 D475 A476 G478 E480 H506 R518 K522 Y526 D654
Binding residue
(residue number reindexed from 1)		R423 D469 A470 G472 E474 H500 R512 K516 Y520 D648
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0004527 exonuclease activity
GO:0004529 DNA exonuclease activity
GO:0005515 protein binding
GO:0008408 3'-5' exonuclease activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006302 double-strand break repair
GO:0039693 viral DNA genome replication
GO:0090592 DNA synthesis involved in DNA replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1tkd, PDBe:1tkd, PDBj:1tkd
PDBsum1tkd
PubMed15297882
UniProtP00581|DPOL_BPT7 DNA-directed DNA polymerase (Gene Name=5)

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