Structure of PDB 4f3o Chain D Binding Site BS03

Receptor Information
>4f3o Chain D (length=579) Species: 235909 (Geobacillus kaustophilus HTA426) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLR
PETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLA
AYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHL
VRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDT
KRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVL
KKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRP
ATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDW
LIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEV
TPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVK
RYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQ
GSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRL
VPEVMEQAVTLRVPLKVDYHYGSTWYDAK
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 chain4f3o Chain D Residue 901 [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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PDB4f3o Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		S655 Q656 H682 R702 K706 A707 Y710 D830
Binding residue
(residue number reindexed from 1)		S358 Q359 H385 R405 K409 A410 Y413 D533
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0008408 3'-5' exonuclease activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4f3o, PDBe:4f3o, PDBj:4f3o
PDBsum4f3o
PubMed
UniProtQ5KWC1

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