Structure of PDB 6dsu Chain A Binding Site BS04

Receptor Information
>6dsu Chain A (length=577) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPE
TALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAY
LLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVR
KAAAIWALERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKR
LEQMGEELAEQLRTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKK
TKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDT
KKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLI
FAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTP
NMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRY
MENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGS
AADIIKKAMIDLNARLKEERLQARLLLQVHDELILEAPKEEMERLCRLVP
EVMEQAVTLRVPLKVDYHYGSTWYDAK
Ligand information
Ligand IDDZ4
InChIInChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
InChIKeyWKIPJDSLGCBQCU-RRKCRQDMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H17 N6 O11 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
ChEMBL
DrugBank
ZINCZINC000032016786
PDB chain6dsu Chain A Residue 905 [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]
PDB6dsu Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		Q656 E658 H682 R702 K706 V713 Y714 Q797 D830
Binding residue
(residue number reindexed from 1)		Q357 E359 H383 R403 K407 V414 Y415 Q498 D531
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
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:0004518 nuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0046872 metal ion binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006974 DNA damage response
GO:0071897 DNA biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6dsu, PDBe:6dsu, PDBj:6dsu
PDBsum6dsu
PubMed30338759
UniProtE1C9K5

[Back to BioLiP]