Structure of PDB 6xi9 Chain B Binding Site BS01

Receptor Information

>6xi9 Chain B (length=380) Species: 485917 (Pedobacter heparinus DSM 2366)

GTENLYFQSMDTTSKLALILADADLPAALKAIALKVQNQERITFDEGVYL
YENAELGYLGVLANYIREQKHGDNTYFNRNFHIEPTNVCVYDCKFCSYSR
LIKQKEEGWEMSVDGMMEVLKKYDHEPVTEVHITGGVVPKQNLEFYSDFF
RRAKAHRPELHIKALTPVEYYYIFKKAKLSHYDGMKYMQEAGLDSMPGGG
AEIFHPEVREKIAHDKCNAEQWLDIHEQAHKLGMKTNATMLYGHIEQFWH
RVDHMERLRRQQDKTGGFQAFIPLKFRNQHNQMDHVPEVSVIEDLRNYAI
ARIYMDNFDHIKAYWAMISRQTAQLSLNFGVDDIDGTLDDTTKIYPAMST
RDLVDLIKQVKRKPIERDTLYNVVTDYSQV

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: 6xi9 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xi9 Narrow-Spectrum Antibiotic Targeting of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis.
• Resolution: 2.14 Å
• Binding residue (original residue number in PDB): C80 Y82 C84 C87 K207
• Binding residue (residue number reindexed from 1): C89 Y91 C93 C96 K216
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.5.1.120: aminodeoxyfutalosine synthase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005506 iron ion binding
• GO:0016740 transferase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
• GO:0044689 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0102573 aminodeoxyfutalosine synthase activity

Biological Process

• GO:0009234 menaquinone biosynthetic process

External links

• PDB: RCSB:6xi9, PDBe:6xi9, PDBj:6xi9
• PDBsum: 6xi9
• PubMed: 32627538
• UniProt: C6XW09