SMTL ID : 6rgz.1

Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 6.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 19 residues within 4Å: Chain A: N.145, N.149, K.152, Y.153, D.180, G.184, I.185, I.193, Y.198, R.199, V.200, G.210, T.211, G.212, L.213, G.214, L.215, S.239, F.241 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.145, A:N.149, A:Y.153, A:D.180, A:R.199, A:V.200, A:T.211, A:G.212, A:L.215, A:S.239 Water bridges: A:K.152, A:K.152, A:Y.153, A:V.200, A:T.211, A:L.213 Salt bridges: A:K.152, A:R.199 pi-Stacking: A:Y.153, A:Y.153 ADP.5: 19 residues within 4Å: Chain B: N.145, N.149, K.152, Y.153, D.180, G.184, I.185, I.193, Y.198, R.199, V.200, G.210, T.211, G.212, L.213, G.214, L.215, S.239, F.241 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:N.145, B:N.149, B:Y.153, B:D.180, B:R.199, B:V.200, B:T.211, B:T.211, B:G.212, B:G.214, B:L.215, B:S.239 Water bridges: B:K.152, B:K.152, B:Y.153, B:V.200, B:L.213, B:L.213 Salt bridges: B:K.152, B:R.199 pi-Stacking: B:Y.153, B:Y.153

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

SO4.2: 2 residues within 4Å: Chain A: H.70, N.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.73 Water bridges: A:H.70 Salt bridges: A:H.70 SO4.3: 3 residues within 4Å: Chain A: N.73, R.140, L.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.73 Salt bridges: A:R.140 SO4.4: 5 residues within 4Å: Chain A: K.39, E.43 Chain B: N.69 Chain D: S.108, Q.111 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Salt bridges: A:K.39 Hydrogen bonds: D:Q.111, B:N.69 SO4.6: 8 residues within 4Å: Chain A: H.29 Chain B: L.79, R.83 Chain D: A.84, K.85, G.86, G.87, D.90 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: D:G.86, D:G.87 Salt bridges: D:K.85, A:H.29, B:R.83 SO4.7: 7 residues within 4Å: Chain A: L.79 Chain B: H.29 Chain C: A.84, K.85, G.86, G.87, D.90 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Water bridges: B:H.29 Salt bridges: B:H.29 Hydrogen bonds: C:G.86, C:G.87 SO4.8: 5 residues within 4Å: Chain A: N.69 Chain B: K.39, E.43 Chain C: S.108, Q.111 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:E.43, C:Q.111, A:N.69 Salt bridges: B:K.39 SO4.9: 3 residues within 4Å: Chain B: I.16, E.195, Q.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.196, B:Q.196 Water bridges: B:R.15 SO4.10: 3 residues within 4Å: Chain B: N.69, H.70, N.73 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.73 Water bridges: B:H.70, B:N.148 Salt bridges: B:H.70 SO4.13: 5 residues within 4Å: Chain B: S.115 Chain C: D.10, S.11, A.12, V.13 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.11, C:A.12, C:V.13, B:S.115, B:S.115 Water bridges: B:Q.67 SO4.14: 3 residues within 4Å: Chain C: V.102, M.103, R.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.104 Salt bridges: C:R.104 SO4.15: 7 residues within 4Å: Chain A: R.83, R.86, S.88 Chain C: G.87, E.88, E.89, D.90 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.88, C:E.89, C:E.89 Salt bridges: A:R.83, A:R.86 SO4.17: 4 residues within 4Å: Chain A: S.115 Chain D: S.11, A.12, V.13 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:S.11, D:A.12, D:V.13, A:S.115, A:S.115 SO4.18: 3 residues within 4Å: Chain D: V.102, M.103, R.104 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.104 Salt bridges: D:R.104 SO4.19: 6 residues within 4Å: Chain B: R.83, S.88 Chain D: G.87, E.88, E.89, D.90 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:E.88, D:E.89, D:D.90, B:S.88, B:S.88

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

CL.11: 1 residues within 4Å: Chain B: R.140 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain C: D.10, D.53, M.55 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:M.55, H2O.5, H2O.6 MG.16: 4 residues within 4Å: Chain D: D.9, D.10, D.53, M.55 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:M.55, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mideros-Mora, C. et al., Revisiting the pH-gated conformational switch on the activities of HisKA-family histidine kinases. Nat Commun (2020)

Release Date

2020-02-19

Peptides

Sensor histidine kinase: AB
Response regulator: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Sensor histidine kinase

Response regulator

Related Entries With Identical Sequence