Structure of PDB 2zim Chain A Binding Site BS01

Receptor Information
>2zim 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]
PALTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEEREN
YLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDELSKQIFRVDKN
FCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTM
LNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGD
LELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSE
SYYNGISTNL
Ligand information
Ligand IDYLY
InChIInChI=1S/C22H35N8O9P/c1-11-5-7-25-14(11)20(33)26-6-3-2-4-12(23)22(34)39-40(35,36)37-8-13-16(31)17(32)21(38-13)30-10-29-15-18(24)27-9-28-19(15)30/h9-14,16-17,21,25,31-32H,2-8,23H2,1H3,(H,26,33)(H,35,36)(H2,24,27,28)/t11-,12-,13+,14+,16+,17-,21-/m1/s1
InChIKeyMLNCIGVKMPQTPJ-CWEHIGOWSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NCCCCC(N)C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C4NCCC4C
OpenEye OEToolkits 1.5.0CC1CCNC1C(=O)NCCCCC(C(=O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)N
OpenEye OEToolkits 1.5.0C[C@@H]1CCN[C@@H]1C(=O)NCCCC[C@H](C(=O)O[P@](=O)(O)OC[C@H]2[C@@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)N
CACTVS 3.341C[C@@H]1CCN[C@@H]1C(=O)NCCCC[C@@H](N)C(=O)O[P@@](O)(=O)OC[C@@H]2O[C@H]([C@H](O)[C@H]2O)n3cnc4c(N)ncnc34
CACTVS 3.341C[CH]1CCN[CH]1C(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34
FormulaC22 H35 N8 O9 P
Name(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HYDROGEN (R)-PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000016052422
PDB chain2zim Chain A Residue 1 [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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PDB2zim Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
M300 A302 L305 Y306 R330 E332 L339 F342 M344 N346 Y384 E396 L397 S398 S399 W417 G419 G421 G423
Binding residue
(residue number reindexed from 1)
M106 A108 L111 Y112 R136 E138 L145 F148 M150 N152 Y190 E202 L203 S204 S205 W223 G225 G227 G229
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:2zim, PDBe:2zim, PDBj:2zim
PDBsum2zim
PubMed17592110
UniProtQ8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)

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