SMTL ID : 8vc9.3 (2 other biounits)

Hybrid response regulator LvrB from Leptospira / phosphorylated REC form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 22 residues within 4Å: Chain A: Q.145, K.148, N.274, A.275, S.278, D.313, T.316, I.318, I.326, F.331, T.332, T.333, K.334, G.339, T.340, G.341, L.342, G.343, L.344, T.368, F.370 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.148, A:K.148, A:N.274, A:S.278, A:D.313, A:T.332, A:T.333, A:T.333, A:K.334, A:G.341, A:L.342, A:G.343, A:L.344, A:T.368 ACP.8: 21 residues within 4Å: Chain B: Q.145, K.148, N.274, S.278, D.313, T.316, I.318, I.326, F.331, T.332, T.333, K.334, G.339, T.340, G.341, L.342, G.343, L.344, T.368, F.370 Ligands: MG.11 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.145, B:K.148, B:K.148, B:N.274, B:S.278, B:D.313, B:T.332, B:T.333, B:T.333, B:T.340, B:G.341, B:L.342, B:G.343, B:L.344, B:T.368 Water bridges: B:K.334, B:K.334

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.11, D.56, S.58 Ligands: BEF.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.11, A:D.56, A:S.58, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain A: N.274 Ligands: ACP.1 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: D.11, D.56, S.58 Ligands: BEF.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.11, B:D.56, B:S.58, H2O.1, H2O.1 MG.11: 2 residues within 4Å: Chain B: N.274 Ligands: ACP.8 No protein-ligand interaction detected (PLIP)

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.3: 8 residues within 4Å: Chain A: D.56, F.57, S.58, S.84, G.85, T.86, K.106 Ligands: MG.2 No protein-ligand interaction detected (PLIP) BEF.10: 8 residues within 4Å: Chain B: D.56, F.57, S.58, S.84, G.85, T.86, K.106 Ligands: MG.9 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: R.195 Chain B: K.179 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.195, B:K.179 SO4.6: 5 residues within 4Å: Chain A: R.260, E.261, G.262, Q.263 Chain B: Q.142 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.262, A:Q.263, B:Q.142 SO4.7: 2 residues within 4Å: Chain A: K.179 Chain B: R.195 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.195, A:K.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agustoni, E. et al., Coiled coil formation and symmetry breaking activates the Leptospira virulence regulator LvrB, a hybrid response regulator. To Be Published

Release Date

2024-12-18

Peptides

Leptospira virulence regulator B (LvrB): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Leptospira virulence regulator B (LvrB)

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