SMTL ID : 6rgy.2 (1 other biounit)

Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 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, I.183, G.184, I.185, I.193, Y.198, R.199, V.200, G.210, T.211, G.212, G.214, L.215, S.239, F.241 22 PLIP interactions: 22 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:V.200, A:T.211, A:T.211, A:G.212, A:L.215, A:S.239 Water bridges: A:K.152, A:K.152, A:Y.153, A:Y.153, A:G.182, A:L.213, A:L.213 Salt bridges: A:K.152, A:R.199 pi-Stacking: A:Y.153

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

SO4.2: 3 residues within 4Å: Chain A: K.39 Chain B: S.108, Q.111 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.39 SO4.3: 2 residues within 4Å: Chain A: R.83, S.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88, A:S.88 Salt bridges: A:R.83 SO4.4: 3 residues within 4Å: Chain A: K.14, E.195, Q.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.196, A:Q.196 Salt bridges: A:K.14 SO4.6: 7 residues within 4Å: Chain A: H.29 Chain B: A.84, K.85, G.86, G.87, D.90 Ligands: CIT.10 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.86, B:G.87 Water bridges: B:D.90, B:D.90 Salt bridges: A:H.29 SO4.7: 3 residues within 4Å: Chain B: V.102, M.103, R.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.104, B:R.104 Salt bridges: B:R.104 SO4.8: 4 residues within 4Å: Chain B: D.10, S.11, A.12, V.13 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.11, B:A.12, B:V.13 Water bridges: A:Q.67 SO4.9: 4 residues within 4Å: Chain B: G.87, E.88, E.89, D.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.88, B:E.89, B:D.90

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: D.9, D.10, D.53, M.55 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:M.55, H2O.5, H2O.5

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.10: 3 residues within 4Å: Chain A: H.29 Chain B: K.85 Ligands: SO4.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.85 Salt bridges: B:K.85, B:K.85, A:H.29

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

Osmosensitive K+ channel histidine kinase KdpD: A
Response regulator: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Osmosensitive K+ channel histidine kinase KdpD

Response regulator

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