SMTL ID : 7pv7.2 (1 other biounit)

Crystal structure of dimeric Porphyromonas gingivalis PorX, a type 9 secretion system response regulator.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

4 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)(Non-covalent)

BEF.1: 9 residues within 4Å: Chain A: D.20, D.63, E.64, N.65, T.91, K.92, S.93, K.113 Ligands: MG.2 No protein-ligand interaction detected (PLIP) BEF.11: 7 residues within 4Å: Chain A: D.244, N.245, A.276, T.277, H.421, H.505 Ligands: ZN.3 No protein-ligand interaction detected (PLIP) BEF.12: 8 residues within 4Å: Chain B: D.20, D.63, E.64, N.65, T.91, K.92, K.113 Ligands: MG.13 No protein-ligand interaction detected (PLIP) BEF.23: 10 residues within 4Å: Chain B: D.244, A.276, T.277, Q.278, D.366, H.421, H.505 Ligands: ZN.14, ZN.15, GOL.19 No protein-ligand interaction detected (PLIP)

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.20, D.63, N.65, M.66 Ligands: BEF.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, A:D.63, A:N.65, H2O.3, H2O.6 MG.9: 7 residues within 4Å: Chain A: K.461, D.462, P.463, L.473, S.474, D.475, K.476 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.461, A:L.473, A:D.475, H2O.5 MG.10: 4 residues within 4Å: Chain A: M.66, G.68, I.69, G.70 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.66, A:G.68, H2O.7, H2O.8 MG.13: 7 residues within 4Å: Chain B: D.20, E.21, D.63, N.65, M.66, K.92 Ligands: BEF.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.20, B:D.63, B:N.65, H2O.15, H2O.18 MG.22: 4 residues within 4Å: Chain B: M.66, G.68, I.69, G.70 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.68, H2O.22

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.244, N.245, T.277, D.420, H.421 Ligands: BEF.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.244, A:T.277, A:D.420, A:H.421 ZN.14: 6 residues within 4Å: Chain B: D.244, N.245, T.277, D.420, H.421 Ligands: BEF.23 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.244, B:D.244, B:T.277, B:D.420, B:H.421 ZN.15: 7 residues within 4Å: Chain B: N.245, D.366, H.370, H.421, H.505 Ligands: GOL.19, BEF.23 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.366, B:D.366, B:H.370, B:H.505

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: T.14, Q.38, T.40, N.55, D.56, F.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.38, A:T.40, A:N.55, A:D.56 GOL.5: 7 residues within 4Å: Chain A: R.319, I.322, E.323, K.327, H.328, Y.329, F.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.319, A:K.327, A:Y.329 GOL.6: 8 residues within 4Å: Chain A: T.440, L.442, K.445, F.486, A.487, Y.488, Y.495, Y.499 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.440, A:K.445, A:Y.488 GOL.7: 8 residues within 4Å: Chain A: P.213, D.214, R.216, P.217, T.218, D.222, K.225, Q.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.213, A:R.216, A:K.225, A:Q.226 Water bridges: A:D.222 GOL.16: 6 residues within 4Å: Chain B: L.24, L.25, H.28, K.113, P.114, V.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.28, B:V.115, B:V.115 Water bridges: B:K.113 GOL.17: 6 residues within 4Å: Chain B: T.14, Q.38, T.40, N.55, D.56, F.57 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.40, B:N.55, B:N.55, B:D.56 Water bridges: B:T.14 GOL.18: 7 residues within 4Å: Chain B: H.370, T.373, D.374, T.440, L.442, Y.499, Q.504 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.370, B:Q.504, B:Q.504 Water bridges: B:Y.499 GOL.19: 8 residues within 4Å: Chain B: A.276, H.370, T.440, N.441, Y.444, H.505 Ligands: ZN.15, BEF.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.441, B:H.505 Water bridges: B:H.505 GOL.20: 7 residues within 4Å: Chain B: R.11, P.12, Y.13, K.35, G.36, Y.37, Q.129 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.13, B:K.35, B:G.36, B:Q.129 Water bridges: B:Y.37, B:Y.37, B:Q.129

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

FMT.8: 5 residues within 4Å: Chain A: L.25, H.28, K.113, P.114, V.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.28, A:V.115 FMT.21: 6 residues within 4Å: Chain B: R.372, R.379, Y.498, R.500, N.501, T.502 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.498 Water bridges: B:R.379

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
B

B
A

Response regulator

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