SMTL ID : 6ev0.1

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (AC129)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x BYK: [(3~{R})-3-carboxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium(Non-covalent)

BYK.1: 15 residues within 4Å: Chain A: I.47, Q.63, Y.64, Y.65, K.66, F.69, K.124, Y.128, I.151, L.152, V.155, Y.156, W.226, F.227, C.231 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.47, A:Y.64, A:K.66, A:I.151 Water bridges: A:K.66, A:K.66 Salt bridges: A:K.66 pi-Stacking: A:W.226 BYK.3: 12 residues within 4Å: Chain B: Q.63, Y.64, Y.65, K.66, F.69, K.124, Y.128, I.151, L.152, V.155, W.226, C.231 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.64, B:I.151, B:L.152 Salt bridges: B:K.66, B:K.124

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

IPA.2: 6 residues within 4Å: Chain A: Y.65, I.71, M.72, Q.125 Chain B: V.126, L.130 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.126, B:L.130 Hydrogen bonds: A:Q.125 IPA.5: 7 residues within 4Å: Chain A: V.126, L.130 Chain B: L.50, Y.65, M.72, V.82, Y.85 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.85, A:V.126, A:L.130 Hydrogen bonds: B:Y.65

1 x C8N: [(3~{S})-3-carboxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium(Non-covalent)

C8N.4: 10 residues within 4Å: Chain A: L.62, Q.63, S.129, K.132, F.133, F.136, S.144 Chain B: S.129, K.132, F.133 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:K.132, A:K.132, A:F.133, A:F.133, A:F.136, B:K.132, B:K.132 Hydrogen bonds: A:Y.128, A:S.144 Salt bridges: A:K.132 pi-Stacking: A:F.133, B:F.133, B:F.133

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

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