SMTL ID : 7pvk.1 (1 other biounit)

X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x G- G: pGpG(Non-covalent)

G-G.1: 20 residues within 4Å: Chain A: D.244, A.276, A.277, Q.278, R.281, E.307, E.308, G.309, K.310, N.311, L.312, K.335, Y.337, N.363, D.366, H.370, H.421, H.505 Ligands: ZN.5, ZN.6 Protein-ligand interaction information (PLIP) not available G-G.2: 22 residues within 4Å: Chain B: D.244, A.276, A.277, Q.278, R.281, E.307, E.308, G.309, K.310, N.311, L.312, K.335, Y.337, N.363, D.366, M.367, H.370, D.420, H.421, H.505 Ligands: ZN.17, ZN.24 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.20, D.63, N.65, M.66, K.92 Ligands: BEF.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.20, A:D.20, A:D.63, A:N.65, H2O.1 MG.15: 6 residues within 4Å: Chain B: D.19, D.20, D.63, N.65, M.66 Ligands: BEF.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.20, B:D.20, B:D.63, B:N.65, H2O.4

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.4: 8 residues within 4Å: Chain A: D.20, D.63, E.64, N.65, T.91, K.92, K.113 Ligands: MG.3 No protein-ligand interaction detected (PLIP) BEF.16: 8 residues within 4Å: Chain B: D.20, D.63, E.64, N.65, T.91, K.92, K.113 Ligands: MG.15 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: D.244, N.245, A.277, D.420, H.421 Ligands: G-G.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.244, A:D.244, A:D.420, A:H.421 ZN.6: 6 residues within 4Å: Chain A: N.245, D.366, H.370, H.421, H.505 Ligands: G-G.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.366, A:H.370, A:H.505 ZN.17: 6 residues within 4Å: Chain B: D.244, N.245, A.277, D.420, H.421 Ligands: G-G.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.244, B:D.244, B:D.420, B:H.421 ZN.24: 6 residues within 4Å: Chain B: N.245, D.366, H.370, H.421, H.505 Ligands: G-G.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.366, B:D.366, B:H.370, B:H.505

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: L.128, Q.129, Q.130, H.131, S.132 Chain B: E.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.128, A:H.131, A:S.132 GOL.8: 7 residues within 4Å: Chain A: P.213, D.214, T.215, R.216, D.222, K.225, Q.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.214, A:K.225, A:Q.226 GOL.9: 9 residues within 4Å: Chain A: R.372, T.373, R.379, Q.497, Y.498, Y.499, R.500, N.501, T.502 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.372, A:R.379, A:Y.498, A:Y.498, A:R.500 GOL.10: 6 residues within 4Å: Chain A: E.188, K.191, N.384, E.385, Q.425, K.427 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.385, A:K.427 GOL.11: 7 residues within 4Å: Chain A: E.64, N.65, M.66, G.68, I.69, G.70, G.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:N.65 GOL.18: 6 residues within 4Å: Chain B: N.127, L.128, Q.129, Q.130, H.131, S.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.131, B:S.132 GOL.19: 7 residues within 4Å: Chain B: P.213, D.214, T.215, R.216, T.218, K.225, Q.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.215, B:Q.226 GOL.20: 9 residues within 4Å: Chain B: R.372, T.373, R.379, Q.497, Y.498, Y.499, R.500, N.501, T.502 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.372, B:T.373, B:R.379, B:R.379, B:N.501 GOL.21: 6 residues within 4Å: Chain B: L.450, D.451, Y.452, P.454, E.459, K.476 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.451 GOL.22: 7 residues within 4Å: Chain A: P.83, Y.84 Chain B: F.171, E.175, E.252, K.255, S.256 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.255 Water bridges: B:E.175, B:S.256, A:K.79

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.12: 5 residues within 4Å: Chain A: E.236, K.237, G.412, K.414, Q.521 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.236, A:K.237, A:Q.521, A:Q.521 FMT.13: 8 residues within 4Å: Chain A: F.57, D.58, I.59, Y.84, T.85, P.86, L.128 Chain B: K.523 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.85, B:K.523 FMT.14: 4 residues within 4Å: Chain A: L.24, K.92, K.113, P.114 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.113 FMT.23: 3 residues within 4Å: Chain B: Y.494, Q.497, Y.498 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitz, C. et al., Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors. Nucleic Acids Res. (2022)

Release Date

2022-12-14

Peptides

Response regulator: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Response regulator

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