Structure of PDB 8vpg Chain B

Receptor sequence

>8vpgB (length=551) Species: 1496 (Clostridioides difficile) [Search protein sequence]

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

3D structure

PDB

8vpg Quinoline-based compounds can inhibit diverse enzymes that act on DNA

Chain

Resolution

3.05 Å

3D
structure

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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 P166 Y168 H171 K173 K193 Y221 S227 F253 I256 G257 F345 Q346 R432 W439 R441 K456 Y476 K511 M513 S514 Y521 P522 N523	Y4 N139 P140 Y142 H145 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 C352 D353 K378 S379 K380 K420 R425 Q438 W439 Y455 K456	H145 K146 K153 D166 K167 K228 I323 G325 C326 D327 K352 S353 K354 K394 R399 Q412 W413 Y429 K430

External links

PDB	RCSB:8vpg, PDBe:8vpg, PDBj:8vpg
PDBsum	8vpg
PubMed
UniProt	A0A031WG99

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