SMTL ID : 7nnp.1

Rb-loaded cryo-EM structure of the E1-ATP KdpFABC complex.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

8 x RB: RUBIDIUM ION(Non-covalent)

RB.1: 4 residues within 4Å: Chain A: I.421, V.538 Chain D: V.231 Ligands: RB.2 No protein-ligand interaction detected (PLIP) RB.2: 5 residues within 4Å: Chain A: Q.367, I.368, F.386, P.425 Ligands: RB.1 No protein-ligand interaction detected (PLIP) RB.3: 1 residues within 4Å: Chain A: G.369 No protein-ligand interaction detected (PLIP) RB.4: 4 residues within 4Å: Chain A: S.343, E.370, S.378, N.465 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.465 RB.5: 4 residues within 4Å: Chain A: N.112, T.230, S.343, N.466 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.343 RB.6: 9 residues within 4Å: Chain A: N.112, T.113, T.230, N.231, D.232, S.343, C.344, N.466, N.467 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:N.112, A:S.343, A:C.344, A:N.467 RB.8: 2 residues within 4Å: Chain A: L.389 Chain D: L.228 No protein-ligand interaction detected (PLIP) RB.11: 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.7: 16 residues within 4Å: Chain A: F.6, I.9, 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 Ligands: CDL.10 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.6, A:I.9, A:L.13, A:V.15, A:M.17, A:F.268, A:F.268, A:L.284, A:W.285, A:W.285, A:W.285, A:V.292, A:V.292, A:V.292 Hydrogen bonds: A:R.21, A:R.21 Salt bridges: A:R.21, A:R.21, A:R.281, A:R.281 CDL.10: 18 residues within 4Å: Chain A: W.285, V.289, G.524, P.525, L.526, V.528, G.529, L.530, I.532, G.533, T.534, L.537 Chain D: S.647, R.651, L.654, W.655, G.658 Ligands: CDL.7 20 PLIP interactions: 8 interactions with chain D, 12 interactions with chain A Hydrophobic interactions: D:R.651, D:L.654, D:L.654, D:L.654, D:W.655, A:W.285, A:W.285, A:W.285, A:W.285, A:V.289, A:P.525, A:P.525, A:L.526, A:V.528, A:L.530, A:I.532 Hydrogen bonds: D:S.647, D:S.647, D:R.651, A:L.526

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

ACP.9: 22 residues within 4Å: Chain D: D.172, D.307, T.309, R.317, D.344, T.346, E.348, F.377, R.382, S.384, K.395, G.396, S.397, T.429, L.431, T.471, G.472, D.473, K.499, D.518, N.521, D.522 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:D.307, D:T.309, D:T.309, D:R.317, D:R.317, D:T.346, D:E.348, D:E.348, D:T.471, D:G.472, D:G.472, D:K.499, D:N.521 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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