Structure of PDB 6xi9 Chain B

Receptor sequence

>6xi9B (length=380) Species: 485917 (Pedobacter heparinus DSM 2366)

GTENLYFQSMDTTSKLALILADADLPAALKAIALKVQNQERITFDEGVYL
YENAELGYLGVLANYIREQKHGDNTYFNRNFHIEPTNVCVYDCKFCSYSR
LIKQKEEGWEMSVDGMMEVLKKYDHEPVTEVHITGGVVPKQNLEFYSDFF
RRAKAHRPELHIKALTPVEYYYIFKKAKLSHYDGMKYMQEAGLDSMPGGG
AEIFHPEVREKIAHDKCNAEQWLDIHEQAHKLGMKTNATMLYGHIEQFWH
RVDHMERLRRQQDKTGGFQAFIPLKFRNQHNQMDHVPEVSVIEDLRNYAI
ARIYMDNFDHIKAYWAMISRQTAQLSLNFGVDDIDGTLDDTTKIYPAMST
RDLVDLIKQVKRKPIERDTLYNVVTDYSQV

3D structure

• PDB: 6xi9 Narrow-Spectrum Antibiotic Targeting of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis.
• Chain: B
• Resolution: 2.14 Å

Enzymatic activity

• Enzyme Commision number: 2.5.1.120: aminodeoxyfutalosine synthase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	SF4	B	C80 Y82 C84 C87 K207	C89 Y91 C93 C96 K216
BS02	MET	B	G126 T157 V159 G191	G135 T166 V168 G200
BS03	V47	B	F86 P188 G190 G191 E193 N228 L232 I263 L265 K266 F267 R268 Y305	F95 P197 G199 G200 E202 N237 L241 I272 L274 K275 F276 R277 Y314

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