Structure of PDB 1skr Chain A Binding Site BS05

Receptor Information
>1skr Chain A (length=669) 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
LTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIDTREYVAGA
PYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRV
DDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNG
AVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGI
DASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTF
IYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLV
EKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVE
KGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWN
FRCLLDTEGKMGPNWAICH
Ligand information
Ligand IDDAD
InChIInChI=1S/C10H16N5O11P3/c11-9-8-10(13-4-12-9)15(5-14-8)7-2-1-6(24-7)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h4-7H,1-3H2,(H,19,20)(H,21,22)(H2,11,12,13)(H2,16,17,18)/t6-,7+/m1/s1
InChIKeyOAKPWEUQDVLTCN-RQJHMYQMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@@H]3CC[C@@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3CC[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CCC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N
FormulaC10 H16 N5 O11 P3
Name2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000012501708
PDB chain1skr Chain A Residue 4004 [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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PDB1skr Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R429 A476 S477 G478 E480 H506 R518 K522 Y526 D654
Binding residue
(residue number reindexed from 1)		R405 A452 S453 G454 E456 H482 R494 K498 Y502 D619
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:1skr, PDBe:1skr, PDBj:1skr
PDBsum1skr
PubMed15235589
UniProtP00581|DPOL_BPT7 DNA-directed DNA polymerase (Gene Name=5)

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