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

1.9 Angstrom crystal structure of dimeric PorX, co-crystallized in the presence of zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.20, D.63, N.65, M.66 Ligands: BEF.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, A:D.63, A:N.65, H2O.7, H2O.9 MG.12: 4 residues within 4Å: Chain A: M.66, P.67, G.68, G.70 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.66, A:G.68, H2O.8, H2O.15 MG.14: 8 residues within 4Å: Chain B: D.19, D.20, E.21, D.63, N.65, M.66, K.92 Ligands: BEF.15 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.20, B:D.63, B:N.65, H2O.24, H2O.25 MG.29: 5 residues within 4Å: Chain B: M.66, P.67, G.68, I.69, G.70 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:M.66, B:G.68, H2O.33, H2O.35, H2O.35 MG.30: 7 residues within 4Å: Chain B: K.461, D.462, P.463, L.473, S.474, D.475, K.476 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.461, B:L.473, B:D.475, H2O.31

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

BEF.2: 7 residues within 4Å: Chain A: D.63, E.64, N.65, T.91, K.92, K.113 Ligands: MG.1 No protein-ligand interaction detected (PLIP) BEF.11: 9 residues within 4Å: Chain A: D.244, A.276, T.277, Q.278, D.366, H.421, H.505 Ligands: ZN.3, ZN.4 No protein-ligand interaction detected (PLIP) BEF.15: 9 residues within 4Å: Chain B: D.20, D.63, E.64, N.65, T.91, K.92, S.93, K.113 Ligands: MG.14 No protein-ligand interaction detected (PLIP) BEF.28: 9 residues within 4Å: Chain B: D.244, N.245, A.276, T.277, R.281, H.421, H.505 Ligands: ZN.16, GOL.21 No protein-ligand interaction detected (PLIP)

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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.244, A:D.244, A:T.277, A:D.420, A:H.421 ZN.4: 6 residues within 4Å: Chain A: N.245, D.366, H.370, H.421, H.505 Ligands: BEF.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.366, A:D.366, A:H.370, A:H.505 ZN.16: 7 residues within 4Å: Chain B: D.244, N.245, T.277, R.281, D.420, H.421 Ligands: BEF.28 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.244, B:T.277, B:D.420, B:H.421

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.12, Y.13, K.35, G.36, Y.37, Q.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.13, A:K.35 Water bridges: A:Y.37 GOL.6: 6 residues within 4Å: Chain A: L.24, 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 GOL.7: 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:N.55, A:D.56 Water bridges: A:T.14 GOL.17: 6 residues within 4Å: Chain B: L.24, L.25, H.28, K.113, P.114, V.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.115 GOL.18: 6 residues within 4Å: Chain B: L.450, D.451, Y.452, P.454, E.459, K.476 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.450, B:Y.452, B:Y.452, B:Y.452, B:K.476 GOL.19: 7 residues within 4Å: Chain A: K.79, K.106, I.107, A.108 Chain B: K.126, Q.130, I.134 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.126, A:A.108 Water bridges: B:Q.130, A:K.79, A:K.79 GOL.20: 4 residues within 4Å: Chain A: E.80 Chain B: R.167, R.168, F.171 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.168, A:E.80, A:E.80 Water bridges: B:E.164, B:F.171 GOL.21: 7 residues within 4Å: Chain B: A.276, T.277, M.368, N.441, Y.444, H.505 Ligands: BEF.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.441, B:H.505 Water bridges: B:T.277, B:N.441

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

FMT.8: 6 residues within 4Å: Chain A: L.128, Q.129, Q.130, H.131, S.132 Chain B: E.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.131, A:H.131, A:S.132, A:S.132 Water bridges: A:Q.130 FMT.9: 4 residues within 4Å: Chain A: L.450, D.451, Y.452, P.454 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.451, A:Y.452 FMT.10: 5 residues within 4Å: Chain A: R.216, P.217, T.218, D.222, Q.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.216 FMT.22: 5 residues within 4Å: Chain B: L.128, Q.129, Q.130, H.131, S.132 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.131, B:S.132, B:S.132, B:S.132 Water bridges: B:Q.130 FMT.23: 7 residues within 4Å: Chain B: T.151, Q.152, S.154, G.155, K.156, L.157, E.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.154 FMT.24: 7 residues within 4Å: Chain B: R.216, P.217, T.218, M.219, D.222, K.225, Q.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.216, B:K.225 FMT.25: 4 residues within 4Å: Chain A: K.255, S.256 Chain B: P.83, Y.84 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.252, A:S.256 FMT.26: 4 residues within 4Å: Chain B: K.237, S.353, M.411, Y.413 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.237 FMT.27: 7 residues within 4Å: Chain B: G.155, K.156, L.157, W.162, L.197, R.200, F.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.201

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 5 residues within 4Å: Chain A: R.207, I.460, K.461, D.462, S.465 Ligand excluded by 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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