Structure of PDB 4ch5 Chain A Binding Site BS01

Receptor Information
>4ch5 Chain A (length=263) 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
HLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDYGDTLDVM
HGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAA
RSESYYNGISTNL
Ligand information
Ligand IDYLP
InChIInChI=1S/C19H30N7O9P/c1-2-12(27)22-6-4-3-5-10(20)19(30)35-36(31,32)33-7-11-14(28)15(29)18(34-11)26-9-25-13-16(21)23-8-24-17(13)26/h8-11,14-15,18,28-29H,2-7,20H2,1H3,(H,22,27)(H,31,32)(H2,21,23,24)/p-1/t10-,11+,14+,15+,18+/m0/s1
InChIKeyDOJLWXPRSAYJFD-MBRXSIFGSA-M
SMILES
SoftwareSMILES
CACTVS 3.385CCC(=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 1.7.6CCC(=O)NCCCC[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.385CCC(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(NCCCCC(N)C(=O)OP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)CC
OpenEye OEToolkits 1.7.6CCC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
FormulaC19 H30 N7 O9 P
Name(S)-2-amino-6-propionamidohexanoic(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride
ChEMBL
DrugBank
ZINC
PDB chain4ch5 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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PDB4ch5 Structural Basis for the Site-Specific Incorporation of Lysine Derivatives Into Proteins.
Resolution2.2 Å
Binding residue
(original residue number in PDB)
R330 E332 H338 L339 F342 M344 N346 E396 L397 S398 S399 W417 G421 G423 R426
Binding residue
(residue number reindexed from 1)
R143 E145 H151 L152 F155 M157 N159 E205 L206 S207 S208 W226 G230 G232 R235
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

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Molecular Function

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Biological Process
External links
PDB RCSB:4ch5, PDBe:4ch5, PDBj:4ch5
PDBsum4ch5
PubMed24760130
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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