Structure of PDB 5tt6 Chain A Binding Site BS01

Receptor Information
>5tt6 Chain A (length=375) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMQELFNNLMELCKDSQRKFFYSDDVSASGRTYRIFSYNYASYSDWLLPD
ALECRGIMFEMDGEKPVRIASRPMEKFFNLNENPFTMNIDLNDVDYILTM
EDGSLVSTYLDGDEILFKSKGSIKSEQALMANGILMNINHHRLRDRLKEL
AEDGFTANFEFVAPTNRIVLAYQEMKIILLNVRENETGEYISYDDIYKDA
TLRPYLVERYEIDSPKWIEEAKNAENIEGYVAVMKDGSHFKIKSDWYVSL
HSTKSSLDNPEKLFKTIIDGASDDLKAMYADDEYSYRKIEAFETTYLKYL
DRALFLVLDCHNKHCGKDRKTYAMEAQGVAKGAGMDHLFGIIMSLYQGYD
SQEKVMCEIEQNFLKNYKKFIPEGY
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5tt6 Chain A Residue 403 [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]
PDB5tt6 Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases.
Resolution2.187 Å
Binding residue
(original residue number in PDB)		Y37 R54 M73 K75 M99 E100 L104 E159 L179 V230 K240 K242
Binding residue
(residue number reindexed from 1)		Y38 R55 M74 K76 M100 E101 L105 E160 L180 V231 K241 K243
Annotation score4
Enzymatic activity
Enzyme Commision number 6.5.1.3: RNA ligase (ATP).
Gene Ontology
Molecular Function
GO:0003972 RNA ligase (ATP) activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0042245 RNA repair
GO:0098004 virus tail fiber assembly

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5tt6, PDBe:5tt6, PDBj:5tt6
PDBsum5tt6
PubMed28223499
UniProtP00971|RLIG_BPT4 RNA ligase 1 (Gene Name=63)

[Back to BioLiP]