Structure of PDB 1xdn Chain A Binding Site BS01

Receptor Information
>1xdn Chain A (length=265) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSDFSPYIEIDLPSESRIQSLHKSGLAAQEWVACEKVHGTNFGIYLINQG
DHEVVRFAKRSGIMDPNENFFGYHILIDEFTAQIRILNDLLKQKYGLSRV
GRLVLNGELFGAKYKHPLVPKSEKWCTLPNGKKFPIAGVQIQREPFPQYS
PELHFFAFDIKYSVSGAEEDFVLLGYDEFVEFSSKVPNLLYARALVRGTL
DECLAFDVENFMTPLPALLGLGNYPLEGNLAEGVVIRHVRRGDPAVEKHN
VSTIIKLRCSSFMEL
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 chain1xdn Chain A Residue 501 [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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PDB1xdn High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1.
Resolution1.2 Å
Binding residue
(original residue number in PDB)		Y58 I59 E60 I61 K87 V88 N92 R111 E159 F209 V286 K307 R309
Binding residue
(residue number reindexed from 1)		Y7 I8 E9 I10 K36 V37 N41 R60 E108 F158 V235 K256 R258
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

View graph for
Molecular Function
External links
PDB RCSB:1xdn, PDBe:1xdn, PDBj:1xdn
PDBsum1xdn
PubMed15465048
UniProtP86927|RLGM1_TRYB2 RNA-editing ligase 1, mitochondrial (Gene Name=REL1)

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