Structure of PDB 6lyb Chain A Binding Site BS03

Receptor Information
>6lyb Chain A (length=260) Species: 2209 (Methanosarcina mazei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEE
RENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQI
FRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEH
LEEFTMLGFQQMGSGCTRENLESIITDFLNHLGIDFKIVGGDTLDVMHGD
LELSSAGVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSE
SYYNGISTNL
Ligand information
Ligand IDEXR
InChIInChI=1S/C11H11NO2S/c12-9(11(13)14)5-7-6-15-10-4-2-1-3-8(7)10/h1-4,6,9H,5,12H2,(H,13,14)/t9-/m1/s1
InChIKeyGAUUPDQWKHTCAX-SECBINFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)c(cs2)CC(C(=O)O)N
OpenEye OEToolkits 2.0.7c1ccc2c(c1)c(cs2)C[C@H](C(=O)O)N
CACTVS 3.385N[CH](Cc1csc2ccccc12)C(O)=O
CACTVS 3.385N[C@H](Cc1csc2ccccc12)C(O)=O
FormulaC11 H11 N O2 S
Name(2R)-2-azanyl-3-(1-benzothiophen-3-yl)propanoic acid;
3-(3-Benzothienyl)-D-alanine
ChEMBL
DrugBank
ZINCZINC000000403160
PDB chain6lyb Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6lyb Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.
Resolution1.90366 Å
Binding residue
(original residue number in PDB)		M300 G419 A420 G421
Binding residue
(residue number reindexed from 1)		M112 G225 A226 G227
Annotation score1
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:6lyb, PDBe:6lyb, PDBj:6lyb
PDBsum6lyb
PubMed32484330
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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