SMTL ID : 7nnl.1

Cryo-EM structure of the KdpFABC complex in an E1-ATP conformation loaded with K+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

10 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: I.421, V.538 Chain D: V.231 Ligands: K.2, K.11 No protein-ligand interaction detected (PLIP) K.2: 3 residues within 4Å: Chain A: Q.367, P.425 Ligands: K.1 No protein-ligand interaction detected (PLIP) K.3: 2 residues within 4Å: Chain A: A.420, T.424 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.420, A:T.424 K.4: 3 residues within 4Å: Chain A: G.369, S.378, G.382 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.369 K.5: 2 residues within 4Å: Chain A: S.378, Y.381 No protein-ligand interaction detected (PLIP) K.6: 5 residues within 4Å: Chain A: N.112, S.343, S.378, N.466, R.493 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.343 K.7: 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.113, A:N.231, A:S.343, A:C.344 K.8: 5 residues within 4Å: Chain A: N.114, G.232, N.239, G.345, G.468 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.232, A:G.468 K.11: 3 residues within 4Å: Chain A: I.421 Chain D: A.227 Ligands: K.1 No protein-ligand interaction detected (PLIP) K.13: 8 residues within 4Å: Chain D: C.261, I.263, T.265, T.266, S.579, D.583, K.586, N.624 No protein-ligand interaction detected (PLIP)

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.9: 18 residues within 4Å: Chain A: F.6, I.9, A.10, L.13, L.14, V.15, M.17, V.18, R.21, F.268, R.281, L.284, W.285, S.288, V.289, V.292, I.293 Ligands: CDL.10 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.6, A:F.6, A:F.6, A:I.9, A:A.10, A:L.13, A:L.13, A:L.14, A:V.15, A:V.15, A:F.268, A:R.281, 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:I.293 Salt bridges: A:R.21, A:R.21, A:R.21, A:R.281, A:R.281 CDL.10: 18 residues within 4Å: Chain A: W.285, I.393, G.524, P.525, L.526, V.528, G.529, L.530, I.532, G.533, T.534, L.537 Chain D: I.580, R.651, L.654, W.655, L.662 Ligands: CDL.9 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:I.393, A:I.393, A:P.525, A:L.526, A:V.528, A:L.530, A:I.532, A:L.537, D:I.580, D:R.651, D:L.654, D:L.654, D:W.655, D:W.655, D:L.662 Hydrogen bonds: A:L.526 Salt bridges: D:R.651

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.12: 20 residues within 4Å: Chain D: N.307, T.309, R.317, D.344, T.346, E.348, F.377, S.384, K.395, S.397, T.429, L.431, T.471, G.472, D.473, K.499, D.518, G.519, N.521, D.522 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:N.307, D:K.308, D:T.309, D:T.309, D:R.317, D:D.344, D:T.346, D:E.348, D:K.395, D:S.397, D:T.471, D:T.471, D:G.472, D:G.472, D:D.473, D:K.499, D:G.519 Salt bridges: D:R.317 pi-Stacking: D:F.377, D:F.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silberberg, J.M. et al., Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC. Nat Commun (2021)

Release Date

2021-07-28

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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