Structure of PDB 6ab2 Chain A Binding Site BS02

Receptor Information
>6ab2 Chain A (length=264) Species: 1293038 (Methanosarcina mazei JCM 9314) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAE
ERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNLSKQIFR
VDKNFCLRPMLAPNLANYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLE
EFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVFGDTLDV
MHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRA
ARSGSYYNGISTNL
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 chain6ab2 Chain A Residue 504 [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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PDB6ab2 Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		R330 E332 H338 L339 F342 E396 L397 S398 S399 G421 G423 R426
Binding residue
(residue number reindexed from 1)		R140 E142 H148 L149 F152 E206 L207 S208 S209 G231 G233 R236
Annotation score5
Enzymatic activity
Enzyme Commision number 6.1.1.26: pyrrolysine--tRNA(Pyl) ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0043039 tRNA aminoacylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ab2, PDBe:6ab2, PDBj:6ab2
PDBsum6ab2
PubMed31031143
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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