SMTL ID : 9oc4.1

High-resolution cryo-EM structure of KdpFABC in the E1P-ADP state in lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 8 residues within 4Å: Chain A: N.112, T.113, T.230, N.231, S.343, C.344, N.466, N.467 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.112, A:T.230, A:N.231, A:S.343, A:C.344 K.6: 6 residues within 4Å: Chain B: V.260, C.261, L.262, I.263, T.265, N.624 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.260, B:C.261, B:I.263, B:T.265, H2O.3

2 x 9Y0: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate(Non-covalent)

9Y0.2: 17 residues within 4Å: Chain A: I.393, H.523, G.524, P.525, L.526, F.527, G.529, L.530, G.533, L.537 Chain B: I.580, S.647, R.651, L.654, G.658, L.659, L.662 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.580, B:R.651, B:L.654, B:L.654, B:L.662, A:L.530, A:L.537 Hydrogen bonds: B:S.647, B:S.647, A:L.526, A:F.527 Salt bridges: B:R.651 9Y0.3: 21 residues within 4Å: Chain A: M.430, A.433, L.434, M.437 Chain B: L.45, I.49, M.58, P.59, A.237, W.240, V.252, V.256, L.259 Chain D: G.4, V.5, T.7, G.8, V.9, L.11, V.12, L.15 14 PLIP interactions: 8 interactions with chain B, 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: B:L.45, B:A.237, B:W.240, B:W.240, B:W.240, B:V.252, B:V.256, B:L.259, D:T.7, D:V.9, D:L.11, D:V.12, D:L.15, A:L.434

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

ADP.4: 20 residues within 4Å: Chain B: D.307, K.308, T.309, R.317, D.344, T.346, E.348, F.377, R.382, S.384, K.395, G.396, S.397, L.431, T.471, G.472, D.473, N.474 Ligands: MG.5, MG.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.309, B:T.309, B:T.309, B:D.344, B:T.346, B:E.348, B:K.395, B:T.471, B:G.472, B:G.472, B:D.473, B:N.474 Salt bridges: B:K.308, B:R.317 pi-Stacking: B:F.377, B:F.377

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 3 residues within 4Å: Chain B: D.307, T.471 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ADP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hussein, A. et al., Conduction pathway for potassium through the E. coli pump KdpFABC. Biorxiv (2025)

Release Date

2025-05-21

Peptides

Potassium-transporting ATPase potassium-binding subunit: A
Potassium-transporting ATPase ATP-binding subunit: B
Potassium-transporting ATPase KdpC subunit: C
Potassium-transporting ATPase KdpF subunit: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Potassium-transporting ATPase potassium-binding subunit

Potassium-transporting ATPase ATP-binding subunit

Potassium-transporting ATPase KdpC subunit

Potassium-transporting ATPase KdpF subunit

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