Structure of PDB 6lyb Chain A Binding Site BS01

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 IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain6lyb Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		R330 E332 H338 L339 F342 E396 L397 S398 S399 G421 G423 R426
Binding residue
(residue number reindexed from 1)		R142 E144 H150 L151 F154 E202 L203 S204 S205 G227 G229 R232
Annotation score3
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:6lyb, PDBe:6lyb, PDBj:6lyb
PDBsum6lyb
PubMed32484330
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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