Structure of PDB 8vph Chain B

Receptor sequence

>8vphB (length=551) Species: 1496 (Clostridioides difficile)

SGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDIL
YDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDS
LTNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEK
KYKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESL
SGKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYID
VFKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETF
YNKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCW
IKSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRE
CKSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVY
SFFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVM
KIRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLG
I

3D structure

• PDB: 8vph Quinoline-based compounds can inhibit diverse enzymes that act on DNA
• Chain: B
• Resolution: 3.18 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	dna	B	Y30 N165 Y168 K173 K193 Y221 S227 F253 I256 G257 F345 Q346 R432 W439 R441 K456 Y476 K511 M513 S514 Y521 P522 N523	Y4 N139 Y142 K147 K167 Y195 S201 F227 I230 G231 F319 Q320 R406 W413 R415 K430 Y450 K485 M487 S488 Y495 P496 N497
BS02	dna	B	H171 K172 K179 D192 K193 K254 I349 G351 D353 K378 K380 K420 R425 Q438 W439 Y455 K456	H145 K146 K153 D166 K167 K228 I323 G325 D327 K352 K354 K394 R399 Q412 W413 Y429 K430
BS03	Q8Y	B	I61 D114 I115 D149 S150 P167 Y178 F200	I35 D88 I89 D123 S124 P141 Y152 F174

External links

• PDB: RCSB:8vph, PDBe:8vph, PDBj:8vph
• PDBsum: 8vph
• UniProt: A0A031WG99