SMTL ID : 7zrd.1

Cryo-EM map of the WT KdpFABC complex in the E1-P tight conformation, stabilised with the inhibitor orthovanadate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

9 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: I.368, P.425, V.538 No protein-ligand interaction detected (PLIP) K.2: 2 residues within 4Å: Chain A: G.369, F.386 No protein-ligand interaction detected (PLIP) K.3: 3 residues within 4Å: Chain A: G.369, T.424 Ligands: K.4 No protein-ligand interaction detected (PLIP) K.4: 4 residues within 4Å: Chain A: Y.381, N.466, G.492 Ligands: K.3 No protein-ligand interaction detected (PLIP) K.5: 4 residues within 4Å: Chain A: I.421, V.538 Chain D: V.231 Ligands: K.10 No protein-ligand interaction detected (PLIP) K.6: 7 residues within 4Å: Chain A: N.112, T.113, T.230, N.231, S.343, N.466, N.467 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.112, A:N.231, A:S.343, A:N.466, A:N.467 K.7: 6 residues within 4Å: Chain A: N.114, Q.116, G.232, N.239, G.345, G.468 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.114 K.10: 3 residues within 4Å: Chain A: I.421 Chain D: L.228 Ligands: K.5 No protein-ligand interaction detected (PLIP) K.11: 5 residues within 4Å: Chain D: C.261, I.263, S.579, D.583, K.586 No protein-ligand interaction detected (PLIP)

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 17 residues within 4Å: Chain A: F.6, I.9, A.10, L.13, L.14, M.17, V.18, R.21, F.268, R.277, R.281, L.284, W.285, S.288, V.289, V.292 Ligands: CDL.9 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.6, A:F.6, A:I.9, A:L.13, A:L.14, A:M.17, A:V.18, A:F.268, A:R.281, A:L.284, A:L.284, A:W.285, A:W.285, A:W.285, A:V.289, A:V.292 Salt bridges: A:R.21, A:R.21, A:R.277, A:R.281, A:R.281, A:R.281, A:R.281 CDL.9: 20 residues within 4Å: Chain A: W.285, I.393, H.523, G.524, P.525, L.526, V.528, G.529, L.530, I.532, G.533, T.534, L.537 Chain D: T.577, S.647, R.651, L.654, W.655, L.659 Ligands: CDL.8 22 PLIP interactions: 13 interactions with chain A, 9 interactions with chain D Hydrophobic interactions: A:W.285, A:W.285, A:W.285, A:I.393, A:P.525, A:P.525, A:L.526, A:L.530, A:I.532, A:L.537, D:T.577, D:L.654, D:L.654, D:W.655, D:W.655, D:L.659 Hydrogen bonds: A:H.523, A:G.524, A:L.526, D:S.647, D:S.647 Salt bridges: D:R.651

1 x VO4: VANADATE ION(Non-covalent)

VO4.12: 9 residues within 4Å: Chain D: L.306, D.307, K.308, T.309, I.470, A.494, K.499, M.515, D.522 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.308, D:T.309, D:T.309, D:T.309, D:K.499, D:K.499

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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