SMTL ID : 7zrk.1

Cryo-EM map of the WT KdpFABC complex in the E1-P_ADP conformation, under turnover conditions

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

12 x K: POTASSIUM ION(Non-covalent)

K.1: 2 residues within 4Å: Chain A: I.421 Ligands: K.2 No protein-ligand interaction detected (PLIP) K.2: 6 residues within 4Å: Chain A: I.421, P.425, V.538, T.542 Ligands: K.1, K.3 No protein-ligand interaction detected (PLIP) K.3: 6 residues within 4Å: Chain A: Q.367, I.368, F.386, P.425 Ligands: K.2, K.9 No protein-ligand interaction detected (PLIP) K.4: 4 residues within 4Å: Chain A: G.369 Ligands: K.5, K.9, K.11 No protein-ligand interaction detected (PLIP) K.5: 5 residues within 4Å: Chain A: G.369, S.378, G.382 Ligands: K.4, K.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.378 K.6: 4 residues within 4Å: Chain A: N.112, S.343, N.466 Ligands: K.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.112, A:S.343 K.7: 9 residues within 4Å: Chain A: N.112, T.113, T.230, N.231, S.343, C.344, G.345, N.466, N.467 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.112, A:T.113, A:N.231, A:S.343, A:N.467 K.8: 6 residues within 4Å: Chain A: N.114, Q.116, G.232, N.239, G.345, G.468 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.232, A:G.345 K.9: 4 residues within 4Å: Chain A: I.421, P.425 Ligands: K.3, K.4 No protein-ligand interaction detected (PLIP) K.10: 6 residues within 4Å: Chain A: S.343, G.374, S.378, N.465, N.466 Ligands: K.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.343 K.11: 3 residues within 4Å: Chain A: G.369 Ligands: K.4, K.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.369 K.15: 5 residues within 4Å: Chain D: C.261, I.263, T.265, K.586, N.624 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:I.263

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 16 residues within 4Å: Chain A: F.6, I.9, A.10, L.13, V.15, M.17, V.18, R.21, F.268, R.281, L.284, W.285, S.288, V.289, V.292 Ligands: CDL.13 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.6, A:F.6, A:I.9, A:L.13, A:V.15, A:V.18, A:F.268, A:L.284, A:W.285, A:W.285, A:W.285, A:W.285, A:V.289, A:V.292, A:V.292, A:V.292 Hydrogen bonds: A:R.21 Salt bridges: A:R.21, A:R.281 CDL.13: 21 residues within 4Å: Chain A: W.285, L.389, I.393, G.524, P.525, L.526, V.528, G.529, L.530, I.532, G.533, T.534, L.537 Chain D: L.228, R.651, L.654, W.655, G.658, L.659, L.662 Ligands: CDL.12 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:W.285, A:W.285, A:W.285, A:W.285, A:L.389, A:V.528, A:V.528, A:L.530, A:I.532, A:I.532, A:L.537, D:L.228, D:R.651, D:L.654, D:L.654, D:L.654, D:W.655, D:L.662 Hydrogen bonds: A:L.526, D:R.651

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

ADP.14: 14 residues within 4Å: Chain D: D.307, T.309, R.317, D.344, T.346, E.348, F.377, A.379, S.384, K.395, G.396, S.397, L.431, D.473 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.344, D:T.346, D:G.349, D:S.384, D:D.473, D:D.473 Salt bridges: D:R.317

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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