Structure of PDB 5d1o Chain A Binding Site BS01

Receptor Information
>5d1o Chain A (length=375) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIPFDLIQERTGVPSSRLKVAFARGSLRLLESAGMQALLFKKPLGDLEAG
TVIYLGDETEVIRGFPKIRRTLLLSPTIQEHFRDRVAVEEKMNGYNVRIA
CLSSGETVALTRGGHVCPFTTRKAQELLDLSEFFREHPDLVICGEMIGRD
NPYVSQDYPEVGPLGFRVFDLREKNTNRPLPVEERRALLDSYGLPNVRLF
GVYPIEEAASEVADIIRALGMAGREGVVMKDPSMEVPPLKYTSSQAHARE
LAYAFSYPFDFGRPFFFSRVIREGFQAYELDESDDETRERARRLGEAIIY
PMLERIKSISAGEAAYEDTVIDVEDREAAEEFIRHLVRLGVSATLADYRD
GRATIRRFYQSTTDRINNYLKGGLY
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 chain5d1o Chain A Residue 401 [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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PDB5d1o Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis.
Resolution2.648 Å
Binding residue
(original residue number in PDB)		F71 K73 I74 E95 E96 K97 M98 N102 R118 E151 F175 V234 K246
Binding residue
(residue number reindexed from 1)		F65 K67 I68 E89 E90 K91 M92 N96 R112 E145 F169 V228 K240
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:5d1o, PDBe:5d1o, PDBj:5d1o
PDBsum5d1o
PubMed26896806
UniProtO27289

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