Structure of PDB 6vt9 Chain A Binding Site BS01

Receptor Information
>6vt9 Chain A (length=335) Species: 5762 (Naegleria gruberi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKLATIRTAGEITPIAGAEAIECCHVDGWTCVIKKGEFKQGDRGVYFEID
SFIKEDNDRYPMLSKQVIDYEGQRGTRLRTARLRGQLSQGLFLPMDRFPE
LASNQVGDDVTEILGITKWEPPISTNLSGEILGEFPTFISKTDQERVQNL
IPQIEENKGQKFEVTVKLDGSSMTVYRKDDHIGVCGRNWELRETATNAQW
HAARRNKMIEGLQFLNRNLALQGAIIGESIQGNLEKLKGQDFYLFDIYDI
DKAQYLTPIERQSLVKQLNDNGFTVKHVPILDDLELNHTAEQILAMADGP
SLNKNVKREGLVFKRLDGKFSFKAISNAYLEKHKD
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 chain6vt9 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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PDB6vt9 Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Resolution2.49 Å
Binding residue
(original residue number in PDB)		K121 D146 Q147 R149 K170 L171 S175 R190 F248 V315 K326
Binding residue
(residue number reindexed from 1)		K118 D143 Q144 R146 K167 L168 S172 R187 F245 V312 K323
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:6vt9, PDBe:6vt9, PDBj:6vt9
PDBsum6vt9
PubMed32315072
UniProtD2W2Z5

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