Structure of PDB 6ab8 Chain A Binding Site BS03

Receptor Information
>6ab8 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 ID9VC
InChIInChI=1S/C14H20N2O4/c15-12(13(17)18)8-4-5-9-16-14(19)20-10-11-6-2-1-3-7-11/h1-3,6-7,12H,4-5,8-10,15H2,(H,16,19)(H,17,18)/t12-/m0/s1
InChIKeyCKGCFBNYQJDIGS-LBPRGKRZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)COC(=O)NCCCCC(C(=O)O)N
OpenEye OEToolkits 2.0.6c1ccc(cc1)COC(=O)NCCCC[C@@H](C(=O)O)N
CACTVS 3.385N[CH](CCCCNC(=O)OCc1ccccc1)C(O)=O
CACTVS 3.385N[C@@H](CCCCNC(=O)OCc1ccccc1)C(O)=O
FormulaC14 H20 N2 O4
Name(2S)-2-azanyl-6-(phenylmethoxycarbonylamino)hexanoic acid
ChEMBL
DrugBank
ZINCZINC000002049231
PDB chain6ab8 Chain A Residue 505 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ab8 Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.
Resolution1.753 Å
Binding residue
(original residue number in PDB)		A306 N346 F384 S399 D408 W417 G421
Binding residue
(residue number reindexed from 1)		A116 N156 F194 S209 D218 W227 G231
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:6ab8, PDBe:6ab8, PDBj:6ab8
PDBsum6ab8
PubMed31031143
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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