SMTL ID : 6t5i.1

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with inhibitor of WNT production (IWP)-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x 9XK: ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide(Non-covalent)

9XK.1: 17 residues within 4Å: Chain A: I.47, Q.63, Y.64, K.66, F.69, K.124, Q.125, Y.128, Q.148, I.151, L.152, Y.156, L.168, N.170, E.175, S.179, W.226 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.47, A:Y.64, A:K.66, A:Y.128, A:L.168 Hydrogen bonds: A:Q.148 pi-Cation interactions: A:K.124

11 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: Q.33, W.34, D.35, P.36, Y.84 No protein-ligand interaction detected (PLIP) DMS.3: 8 residues within 4Å: Chain A: L.50, Y.65, M.72, V.82, Q.125 Chain B: V.126, S.127, L.130 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.127 DMS.4: 3 residues within 4Å: Chain A: N.32, W.34, D.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32 Salt bridges: A:D.35 DMS.5: 4 residues within 4Å: Chain A: D.224, E.225, Y.228, W.235 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.225 Salt bridges: A:D.224 pi-Cation interactions: A:Y.228 DMS.6: 3 residues within 4Å: Chain A: I.30, Y.39, V.98 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.35 pi-Cation interactions: A:Y.39 DMS.7: 6 residues within 4Å: Chain A: Q.120, K.124, L.229, A.230 Chain B: F.75, T.78 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.77 pi-Cation interactions: B:F.75 DMS.9: 8 residues within 4Å: Chain B: Q.63, Y.64, Y.65, F.69, K.124, Q.125, Y.128, W.226 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.128 DMS.10: 5 residues within 4Å: Chain A: F.133 Chain B: L.62, Q.63, Y.128, S.129 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B pi-Cation interactions: A:F.133 Hydrogen bonds: B:Q.63 DMS.11: 7 residues within 4Å: Chain A: V.126, S.127, L.130 Chain B: Y.65, M.72, V.82, Q.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.125 Water bridges: B:M.72 DMS.12: 4 residues within 4Å: Chain B: D.224, E.225, Y.228, W.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.224 Salt bridges: B:D.224 DMS.13: 3 residues within 4Å: Chain B: K.27, L.29, E.88 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.88

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

NA.8: 4 residues within 4Å: Chain A: F.31, N.32, D.35, E.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:Q.37 NA.14: 3 residues within 4Å: Chain B: N.32, D.35, E.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, T.T. et al., Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages. Plos Pathog. (2022)

Release Date

2021-10-27

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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