Structure of PDB 3vqx Chain C Binding Site BS01

Receptor Information
>3vqx Chain C (length=254) Species: 2209 (Methanosarcina mazei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEERENYL
GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDLSKQIFRVDKNF
CLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKGKEHLEEFTMLNFC
QMGSGCTRENLESIITDFLNHLGIDFKIVGCMVYGDTLDVMHGDLELSSA
VVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGI
STNL
Ligand information
Ligand IDBLK
InChIInChI=1S/C21H34N7O10P/c1-21(2,3)37-20(32)24-7-5-4-6-11(22)19(31)38-39(33,34)35-8-12-14(29)15(30)18(36-12)28-10-27-13-16(23)25-9-26-17(13)28/h9-12,14-15,18,29-30H,4-8,22H2,1-3H3,(H,24,32)(H,33,34)(H2,23,25,26)/t11-,12+,14+,15+,18+/m0/s1
InChIKeyXYDQQGDGPLGSGU-URQYDQELSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)(C)OC(=O)NCCCC[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
OpenEye OEToolkits 1.7.6CC(C)(C)OC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.370CC(C)(C)OC(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370CC(C)(C)OC(=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
ACDLabs 12.01O=C(OC(C)(C)C)NCCCCC(N)C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC21 H34 N7 O10 P
Name[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoate
ChEMBL
DrugBank
ZINCZINC000098208702
PDB chain3vqx Chain C Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vqx A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
Resolution2.3 Å
Binding residue
(original residue number in PDB)		A302 Y306 R330 H338 L339 F342 E396 S399 W417 G423 R426
Binding residue
(residue number reindexed from 1)		A107 Y111 R135 H140 L141 F144 E196 S199 W217 G223 R226
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
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Biological Process
External links
PDB RCSB:3vqx, PDBe:3vqx, PDBj:3vqx
PDBsum3vqx
PubMed23275158
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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