Structure of PDB 6p78 Chain A Binding Site BS02

Receptor Information

>6p78 Chain A (length=230) Species: 428126 (Thomasclavelia spiroformis DSM 1552)

SMERYSHILEKDKREIVLLKSRPCIWGKCSFCDYIEDNDVDQKENQKIND
EVLNKITGQYGVLEVINSGSFFELPDETIERIYKIIGEKKIKRLYIEAHY
LYKKKIKALREKFKIEIIVKTGIETFNDEMRNNVLNKNIHFDKIEEILED
FDSPCLMVGIQGQTKEMIRKDIEILTKYFDHGTINIYRNNSTPIKRDEEL
IKWFDEEYHDLKNNRKYDYLGIPTDFGVGD

Ligand information

• Ligand ID: QUG
• InChI: InChI=1S/C12H15N5O3/c13-12-16-10-8(11(20)17-12)5(4-15-10)3-14-6-1-2-7(18)9(6)19/h1-2,4,6-7,9,14,18-19H,3H2,(H4,13,15,16,17,20)/t6-,7-,9-/m0/s1
• InChIKey: WYROLENTHWJFLR-ZKWXMUAHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1c(c2c([nH]1)NC(=NC2=O)N)CNC3C=CC(C3O)O
  OpenEye OEToolkits 2.0.7: c1c(c2c([nH]1)NC(=NC2=O)N)CN[C@H]3C=C[C@@H]([C@H]3O)O
  ACDLabs 12.01: N1=C(Nc3c(C1=O)c(CNC2C(O)C(C=C2)O)cn3)N
  CACTVS 3.385: NC1=NC(=O)c2c(CN[CH]3C=C[CH](O)[CH]3O)c[nH]c2N1
  CACTVS 3.385: NC1=NC(=O)c2c(CN[C@H]3C=C[C@H](O)[C@H]3O)c[nH]c2N1
• Formula: C12 H15 N5 O3
• Name: 2-amino-5-({[(1S,4S,5S)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one;
  Queuine
• PDB chain: 6p78 Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6p78 Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens.
• Resolution: 1.726 Å
• Binding residue (original residue number in PDB): Y33 S67 E96 K119 P222 G228 D229
• Binding residue (residue number reindexed from 1): Y34 S68 E97 K120 P223 G229 D230
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

External links

• PDB: RCSB:6p78, PDBe:6p78, PDBj:6p78
• PDBsum: 6p78
• PubMed: 31481610
• UniProt: B1C2R2