SMTL ID : 6eut.1

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (KSK67)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x BY8: (3~{R})-8-cyclopropyl-7-[(4-methylnaphthalen-1-yl)methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid(Non-covalent)

BY8.1: 14 residues within 4Å: Chain A: Q.63, Y.64, Y.65, K.66, F.69, K.124, Q.125, Y.128, Q.148, I.151, L.152, V.155, W.226, C.231 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.64, A:Y.65, A:K.66, A:F.69, A:Q.125, A:Y.128, A:Q.148, A:I.151, A:I.151, A:W.226 Water bridges: A:K.66, A:K.66 Salt bridges: A:K.66 BY8.4: 14 residues within 4Å: Chain B: I.47, Q.63, Y.64, Y.65, K.66, F.69, K.124, Y.128, Q.148, I.151, L.152, V.155, W.226, C.231 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.47, B:Y.64, B:Y.65, B:K.66, B:F.69, B:Y.128, B:Q.148, B:I.151, B:L.152, B:W.226 Water bridges: B:K.124, B:K.124 Salt bridges: B:K.66

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: N.32, D.35, E.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.32 NA.5: 3 residues within 4Å: Chain B: N.32, D.35, E.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.38

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 8 residues within 4Å: Chain A: L.50, Y.65, I.71, M.72, V.82, Q.125 Chain B: V.126, L.130 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.71, B:V.126, B:L.130 Hydrogen bonds: A:Q.125 Water bridges: A:M.72

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: V.126, S.127, L.130 Chain B: Y.65, I.71, M.72, V.82, Y.85, Q.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.65, B:M.72, B:Q.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kulen, M. et al., Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes. J. Med. Chem. (2018)

Release Date

2018-05-02

Peptides

Listeriolysin regulatory protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Listeriolysin regulatory protein

Related Entries With Identical Sequence