Structure of PDB 4pdk Chain B

Receptor sequence

>4pdkB (length=265) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961)

PAGFAEKYIIESIWNGRFPPGSILPAERELSELIGVTRTTLREVLQRLAR
DGWLTIQHGKPTKVNQFMETSGLHILDTLMTLDAENATSIVEDLLAARTN
ISPIFMRYAFKLNKESAERIMINVIESCEALVNAPSWDAFIAASPYAEKI
QQHVKEDSEKDELKRQEILIAKTFNFYDYMLFQRLAFHSGNQIYGLIFNG
LKKLYDRVGSYYFSNPQARELAMEFYRQLLAVCQSGEREHLPQVIRQYGI
ASGHIWNQMKMTLPS

3D structure

• PDB: 4pdk The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand.
• Chain: B
• Resolution: 2.8 Å

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	3VV	B	W21 I82	W14 I75	PDBbind-CN: -logKd/Ki=8.22,Kd=6nM
BS02	3VV	B	L101 L102 A104 R105 T106 L208 Y212 V215 G216 Y219 R253 G256 I257 S259 G260	L94 L95 A97 R98 T99 L201 Y205 V208 G209 Y212 R246 G249 I250 S252 G253	PDBbind-CN: -logKd/Ki=8.22,Kd=6nM
BS03	3VV	B	R126 N130 Y153 Y184 M187 R191 F194 L203 I204 L208	R119 N123 Y146 Y177 M180 R184 F187 L196 I197 L201	PDBbind-CN: -logKd/Ki=8.22,Kd=6nM

Gene Ontology

Molecular Function

• GO:0000062 fatty-acyl-CoA binding
• GO:0003677 DNA binding
• GO:0003700 DNA-binding transcription factor activity

Biological Process

• GO:0006355 regulation of DNA-templated transcription
• GO:0006631 fatty acid metabolic process
• GO:0019217 regulation of fatty acid metabolic process
• GO:0071072 negative regulation of phospholipid biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4pdk, PDBe:4pdk, PDBj:4pdk
• PDBsum: 4pdk
• PubMed: 25607896
• UniProt: Q9KQU8|FADR_VIBCH Fatty acid metabolism regulator protein (Gene Name=fadR)