Structure of PDB 5d6s Chain B Binding Site BS01

Receptor Information

>5d6s Chain B (length=370) Species: 1308 (Streptococcus thermophilus)

MNIKLEIQKMAKEIGISKIGFTTADDFDYLEKSLRLGVEEGRTTGFEHKN
IEERIYPKLSLESAKTIISIAVAYPHKLPQQPQKTEFKRGKITPNSWGLD
YHYVLQDKLKRLAKGIEKLTENFEYKGMVDTGALVDTAVAKRAGIGFIGK
NGLVISKEYGSYMYLGELITNLEIEPDQEVDYGCGDCRRCLDACPTSCLI
GDGTMNARRCLSFQTQDKGMMDMEFRKKIKTVIYGCDICQISCPYNRGID
NPLDIDPDLAMPELLPFLELTNKSFKETFGMIAGSWRGKNILQRNAIIAL
ANLHDRNAIVKLMEIIDKNNNPIHTATAIWALGEIVKKPDEGMLDYMRGL
SPKDEHSQAEWELVCAKWQI

Ligand information

• Ligand ID: SF4
• InChI: InChI=1S/4Fe.4S
• InChIKey: LJBDFODJNLIPKO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
  CACTVS 3.385: S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
• Formula: Fe4 S4
• Name: IRON/SULFUR CLUSTER
• PDB chain: 5d6s Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d6s Epoxyqueuosine Reductase Structure Suggests a Mechanism for Cobalamin-dependent tRNA Modification.
• Resolution: 2.65 Å
• Binding residue (original residue number in PDB): K150 N151 C184 C187 C190 C243 P244 Y245
• Binding residue (residue number reindexed from 1): K150 N151 C184 C187 C190 C243 P244 Y245
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0052693 epoxyqueuosine reductase activity

Biological Process

• GO:0008033 tRNA processing
• GO:0008616 queuosine biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5d6s, PDBe:5d6s, PDBj:5d6s
• PDBsum: 5d6s
• PubMed: 26378237
• UniProt: A0A0R4I997