Structure of PDB 4ch3 Chain A Binding Site BS01

Receptor Information
>4ch3 Chain A (length=267) Species: 192952 (Methanosarcina mazei Go1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAE
ERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQ
IFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKE
HLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDT
LDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNI
KRAARSESYYNGISTNL
Ligand information
Ligand IDYLB
InChIInChI=1S/C20H32N7O9P/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/h9-12,15-16,19,29-30H,2-8,21H2,1H3,(H,23,28)(H,32,33)(H2,22,24,25)/p-1/t11-,12-,15-,16-,19-/m1/s1
InChIKeyOAECZBFMQNITMX-JCQVVMGJSA-M
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCCCCC(N)C(=O)OP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)CCC
CACTVS 3.385CCCC(=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
OpenEye OEToolkits 1.7.6CCCC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.385CCCC(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.7.6CCCC(=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 H32 N7 O9 P
Name5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine
ChEMBL
DrugBank
ZINC
PDB chain4ch3 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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PDB4ch3 Structural Basis for the Site-Specific Incorporation of Lysine Derivatives Into Proteins.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		R330 E332 L339 F342 M344 E396 L397 S398 S399 G419 A420 G421 G423 R426
Binding residue
(residue number reindexed from 1)		R143 E145 L152 F155 M157 E209 L210 S211 S212 G232 A233 G234 G236 R239
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:4ch3, PDBe:4ch3, PDBj:4ch3
PDBsum4ch3
PubMed24760130
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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