Structure of PDB 4ch4 Chain A Binding Site BS01

Receptor Information
>4ch4 Chain A (length=259) Species: 192952 (Methanosarcina mazei Go1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAE
ERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQ
IFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKEGKEHL
EEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGGDTLDVMHGDL
ELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSES
YYNGISTNL
Ligand information
Ligand IDYLC
InChIInChI=1S/C20H30N7O9P/c1-2-5-13(28)23-7-4-3-6-11(21)20(31)36-37(32,33)34-8-12-15(29)16(30)19(35-12)27-10-26-14-17(22)24-9-25-18(14)27/h2,5,9-12,15-16,19,29-30H,3-4,6-8,21H2,1H3,(H,23,28)(H,32,33)(H2,22,24,25)/p-1/b5-2+/t11-,12-,15-,16-,19-/m1/s1
InChIKeyILVVVZQSKVIFML-XNGPLBMESA-M
SMILES
SoftwareSMILES
CACTVS 3.385CC=CC(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.7.6CC=CC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.385C\C=C\C(=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 12.01O=C(/C=C/C)NCCCCC(N)C(=O)OP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6C/C=C/C(=O)NCCCC[C@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
FormulaC20 H30 N7 O9 P
Name5'-O-[({(2R)-2-amino-6-[(2E)-but-2-enoylamino]hexanoyl}oxy)phosphinato]adenosine
ChEMBL
DrugBank
ZINC
PDB chain4ch4 Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ch4 Structural Basis for the Site-Specific Incorporation of Lysine Derivatives Into Proteins.
Resolution2.16 Å
Binding residue
(original residue number in PDB)		Y306 R330 E332 L339 F342 M344 N346 E396 L397 S398 S399 W417 A420 G421 G423 R426
Binding residue
(residue number reindexed from 1)		Y119 R143 E145 L150 F153 M155 N157 E201 L202 S203 S204 W222 A225 G226 G228 R231
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
View graph for
Biological Process
External links
PDB RCSB:4ch4, PDBe:4ch4, PDBj:4ch4
PDBsum4ch4
PubMed24760130
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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