Structure of PDB 2zio Chain A Binding Site BS02

Receptor Information
>2zio Chain A (length=255) Species: 2209 (Methanosarcina mazei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PALTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEEREN
YLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNLSKQIFRVDKN
FCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGEHLEEFTML
NFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDYGDTLDVMHGDLELSS
AVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNG
ISTNL
Ligand information
Ligand IDAYB
InChIInChI=1S/C20H32N7O10P/c1-2-7-34-20(31)23-6-4-3-5-11(21)19(30)37-38(32,33)35-8-12-14(28)15(29)18(36-12)27-10-26-13-16(22)24-9-25-17(13)27/h9-12,14-15,18,28-29H,2-8,21H2,1H3,(H,23,31)(H,32,33)(H2,22,24,25)/t11-,12+,14+,15+,18+/m0/s1
InChIKeyFNGSPKAFCIGHDI-URQYDQELSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCOC(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341CCCOC(=O)NCCCC[C@H](N)C(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(OCCC)NCCCCC(N)C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0CCCOC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
OpenEye OEToolkits 1.5.0CCCOC(=O)NCCCC[C@@H](C(=O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
FormulaC20 H32 N7 O10 P
Name5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine;
NE-ALLYLOXYCARBONYL-L-LYSINE-5'-ADENOSINE MONOPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000058626689
PDB chain2zio Chain A Residue 601 [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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PDB2zio Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode N(varepsilon)-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification
Resolution2.06 Å
Binding residue
(original residue number in PDB)		A302 R330 E337 L339 F342 M344 N346 E396 L397 S399 V401 W417 A420 G421 G423 R426
Binding residue
(residue number reindexed from 1)		A108 R136 E142 L144 F147 M149 N151 E197 L198 S200 V202 W218 A221 G222 G224 R227
Annotation score2
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
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Biological Process
External links
PDB RCSB:2zio, PDBe:2zio, PDBj:2zio
PDBsum2zio
PubMed19022179
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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