Structure of PDB 2zim Chain A Binding Site BS02

Receptor Information

>2zim Chain A (length=260) Species: 2209 (Methanosarcina mazei)

PALTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEEREN
YLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDELSKQIFRVDKN
FCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTM
LNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGD
LELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSE
SYYNGISTNL

Ligand information

• Ligand ID: POP
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-L
• SMILES:
  OpenEye OEToolkits 1.5.0: O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
  CACTVS 3.341: O[P]([O-])(=O)O[P](O)([O-])=O
  ACDLabs 10.04: [O-]P(=O)(O)OP([O-])(=O)O
  OpenEye OEToolkits 1.5.0: OP(=O)([O-])OP(=O)(O)[O-]
• Formula: H2 O7 P2
• Name: PYROPHOSPHATE 2-
• PDB chain: 2zim Chain A Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2zim Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): H338 E396 R426
• Binding residue (residue number reindexed from 1): H144 E202 R232
• Annotation score: 5

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

External links

• PDB: RCSB:2zim, PDBe:2zim, PDBj:2zim
• PDBsum: 2zim
• PubMed: 17592110
• UniProt: Q8PWY1|PYLS_METMA Pyrrolysine--tRNA ligase (Gene Name=pylS)