SMTL ID : 6exl.1

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (MK206) - folded HTH motif

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x C2Q: [(3~{R})-3-carboxy-7-[(4-methylnaphthalen-1-yl)methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium(Non-covalent)

C2Q.1: 14 residues within 4Å: Chain A: Q.63, Y.64, Y.65, K.66, F.69, K.124, Y.128, Q.148, I.151, L.152, V.155, W.226, F.227, C.231 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.64, A:K.66, A:Y.128, A:Q.148, A:I.151, A:L.152 Hydrogen bonds: A:K.66 Water bridges: A:K.66 Salt bridges: A:K.66 pi-Stacking: A:W.226 C2Q.5: 15 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, F.227, C.231 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.47, B:Y.64, B:K.66, B:Y.128, B:Q.148, B:I.151 Water bridges: B:K.66, B:K.66, B:K.66 Salt bridges: B:K.66, B:K.124 pi-Stacking: B:W.226

3 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:D.35 NA.3: 2 residues within 4Å: Chain A: G.236, N.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.239, A:N.239 NA.6: 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

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

IPA.4: 7 residues within 4Å: Chain A: Y.65, I.71, M.72, V.82, Q.125 Chain B: V.126, L.130 6 PLIP interactions: 4 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, A:Q.125 Water bridges: A:M.72 IPA.7: 8 residues within 4Å: Chain A: V.126, L.130 Chain B: L.50, Y.65, I.71, M.72, V.82, Q.125 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.50, B:I.71, B:V.82, A:V.126, A:L.130 Hydrogen bonds: B:Q.125, B:Q.125 Water bridges: B:M.72

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 positive regulatory factor A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Listeriolysin positive regulatory factor A

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