SMTL ID : 9epn.1

Crystal structure of HprS histidine kinase cytoplasmic fragment from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 20 residues within 4Å: Chain A: N.184, A.185, R.187, Y.188, S.213, I.218, L.224, W.229, R.230, G.231, N.233, S.234, G.239, Q.240, G.241, L.242, G.243, L.244, F.269 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Y.188, A:Y.188, A:S.213, A:S.213, A:R.230, A:G.231, A:G.231, A:N.233, A:S.234, A:Q.240, A:G.241, A:L.242, A:G.243, A:L.244, A:N.267 Water bridges: A:N.184, A:N.184, A:N.184, A:R.187, A:R.187 Salt bridges: A:R.187, A:R.230 AGS.18: 20 residues within 4Å: Chain B: N.184, A.185, R.187, Y.188, S.213, I.218, L.224, W.229, R.230, G.231, N.233, S.234, G.239, Q.240, G.241, L.242, G.243, L.244, F.269 Ligands: MG.19 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.184, B:Y.188, B:S.213, B:S.213, B:R.230, B:G.231, B:N.233, B:S.234, B:S.234, B:Q.240, B:G.241, B:L.242, B:G.243, B:L.244, B:N.267 Water bridges: B:R.187, B:R.187, B:Q.240 Salt bridges: B:R.187, B:R.230

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: N.184 Ligands: AGS.1 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain B: N.184 Ligands: AGS.18 No protein-ligand interaction detected (PLIP)

2 x GCH: GLYCOCHOLIC ACID(Non-covalent)

GCH.3: 15 residues within 4Å: Chain A: M.1, A.2, I.5, R.6, L.9, P.30, H.51, L.54, V.55, F.58 Chain B: D.57, R.60, L.61, D.124 Ligands: EDO.15 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:A.2, A:V.55, A:F.58, A:F.58, A:F.58, B:R.60, B:L.61 Hydrogen bonds: A:H.51, B:D.57, B:D.57, B:R.60 Salt bridges: A:H.51 Water bridges: B:D.124, B:D.124 GCH.20: 9 residues within 4Å: Chain B: Q.166, I.167, F.168, L.201, T.203, S.205, Q.275, R.276, N.277 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Q.166, B:F.168, B:L.201, B:Q.275 Hydrogen bonds: B:S.205, B:R.276, B:N.277

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Chain A: Y.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.147 Water bridges: A:S.179 EDO.5: 5 residues within 4Å: Chain A: H.196, L.263, N.264, H.266, V.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.196, A:L.263 EDO.6: 5 residues within 4Å: Chain A: F.64, D.67, I.117, L.120, R.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.227, A:R.227 EDO.7: 4 residues within 4Å: Chain A: N.138, V.161, E.162, N.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.138, A:V.161 EDO.8: 4 residues within 4Å: Chain A: L.129, D.170, I.172, L.173 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.170, A:I.172 EDO.9: 6 residues within 4Å: Chain A: L.61, F.64, L.118, A.121 Chain B: A.65, A.69 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.65 Water bridges: A:K.125 EDO.11: 3 residues within 4Å: Chain B: F.119, V.128, L.173 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: L.132, L.253, H.254 No protein-ligand interaction detected (PLIP) EDO.13: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.179, B:S.179 EDO.14: 4 residues within 4Å: Chain B: A.69, H.70, R.73, T.74 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.69, B:R.73 Water bridges: B:H.70, B:H.70, B:T.74 EDO.15: 4 residues within 4Å: Chain B: R.60, F.64, R.227 Ligands: GCH.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.60 EDO.16: 3 residues within 4Å: Chain B: H.196, N.264, H.266 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.264 EDO.17: 5 residues within 4Å: Chain A: S.62 Chain B: A.121, R.122, K.125, N.127 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.127, A:S.62

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 2 residues within 4Å: Chain A: S.136, Q.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koczurowska, A. et al., Structural and biophysical characterization of the cytoplasmic domains of HprS kinase and its interactions with the cognate regulator HprR. Arch.Biochem.Biophys. (2024)

Release Date

2025-01-22

Peptides

Sensor histidine kinase HprS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sensor histidine kinase HprS