SMTL ID : 7zri.1

Cryo-EM structure of the KdpFABC complex in a nucleotide-free E1 conformation loaded with K+

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

7 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.1: 5 residues within 4Å: Chain A: N.114, G.233, N.239, G.345, G.468 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.114, A:G.345, A:G.468 K.2: 2 residues within 4Å: Chain A: N.466 Ligands: K.4 No protein-ligand interaction detected (PLIP) K.3: 3 residues within 4Å: Chain A: P.425, V.538, T.542 No protein-ligand interaction detected (PLIP) K.4: 1 residues within 4Å: Ligands: K.2 No protein-ligand interaction detected (PLIP) K.5: 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:N.231, A:S.343, A:C.344, A:N.467 K.7: 2 residues within 4Å: Chain A: I.421 Chain D: A.227 No protein-ligand interaction detected (PLIP) K.9: 6 residues within 4Å: Chain D: C.261, I.263, T.265, S.579, D.583, N.624 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:C.261

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.6: 17 residues within 4Å: Chain A: F.6, I.9, A.10, L.13, M.17, V.18, R.21, F.268, R.277, R.281, L.284, W.285, S.288, V.289, V.292, I.293 Ligands: CDL.8 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.6, A:F.6, A:I.9, A:L.13, A:M.17, A:V.18, A:F.268, A:R.281, A:L.284, A:W.285, A:V.289, A:V.292, A:V.292, A:I.293 Hydrogen bonds: A:R.277, A:R.281 Salt bridges: A:R.21, A:R.21, A:R.21, A:R.281 CDL.8: 21 residues within 4Å: Chain A: W.285, I.393, G.524, P.525, L.526, V.528, G.529, L.530, G.533, T.534, L.537 Chain D: T.577, I.580, S.647, R.651, L.654, W.655, G.658, L.659, L.662 Ligands: CDL.6 18 PLIP interactions: 8 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:I.580, D:L.654, D:W.655, D:L.659, D:L.662, A:W.285, A:W.285, A:W.285, A:I.393, A:P.525, A:P.525, A:V.528, A:V.528, A:L.537 Hydrogen bonds: D:S.647, D:S.647, A:L.526 Salt bridges: D:R.651

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silberberg, J.M. et al., Inhibited KdpFABC transitions into an E1 off-cycle state. Elife (2022)

Release Date

2022-11-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Membrane

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

Potassium-transporting ATPase KdpC subunit

Potassium-transporting ATPase KdpF subunit

Potassium-transporting ATPase ATP-binding subunit

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