Structure of PDB 5w6k Chain A Binding Site BS03

Receptor Information
>5w6k Chain A (length=522) Species: 271 (Thermus aquaticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDL
KEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYG
GEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHVE
ATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLF
DELGLPAIGKTEKTGKRSTSAAVLEALREAHAIVEKILQYRELTKLKSTY
IDPLPELIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIR
RAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASW
MFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPFPKVRAWIEK
TLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAAD
LMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEG
VYPLAVPLEVEVGIGEDWLSAK
Ligand information
Ligand IDA5J
InChIInChI=1S/C10H18N3O15P3/c11-9-5(13(16)17)1-4(10(15)12-9)7-2-6(14)8(26-7)3-25-30(21,22)28-31(23,24)27-29(18,19)20/h1,6-8,14,16-17H,2-3H2,(H,21,22)(H,23,24)(H3,11,12,15)(H2,18,19,20)/t6-,7+,8+/m0/s1
InChIKeyKAFFDRNDCIZAAZ-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1c(c(nc(c1N(O)O)N)O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 2.0.6c1c(c(nc(c1N(O)O)N)O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.385Nc1nc(O)c(cc1N(O)O)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
CACTVS 3.385Nc1nc(O)c(cc1N(O)O)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
ACDLabs 12.01N(c1c(nc(c(c1)C2CC(O)C(O2)COP(=O)(O)OP(O)(=O)OP(=O)(O)O)O)N)(O)O
FormulaC10 H18 N3 O15 P3
Name(1R)-1-[6-amino-5-(dihydroxyamino)-2-hydroxypyridin-3-yl]-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-erythro-pentitol
ChEMBL
DrugBank
ZINC
PDB chain5w6k Chain A Residue 901 [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]
PDB5w6k Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide.
Resolution2.339 Å
Binding residue
(original residue number in PDB)		R573 D610 Y611 S612 Q613 I614 E615 H639 R659 R660 K663 F667 D785
Binding residue
(residue number reindexed from 1)		R278 D315 Y316 S317 Q318 I319 E320 H344 R364 R365 K368 F372 D476
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0001882 nucleoside binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5w6k, PDBe:5w6k, PDBj:5w6k
PDBsum5w6k
PubMed29986111
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

[Back to BioLiP]