SMTL ID : 7n73.1

Cryo-EM structure of ATP13A2 in the ADP-AlF-bound E1P-ADP-like state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: T.510, D.566, M.568, D.569, F.625, S.627, Q.630, R.631, M.632, K.649, G.650, S.651, R.681, V.682, V.683, T.745, G.746, D.747, R.848, N.876 Ligands: ALF.2, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.510, A:D.566, A:D.566, A:K.649, A:V.682, A:G.746, A:D.747, A:D.747, A:D.747, A:R.848, A:R.848, A:N.876 Salt bridges: A:R.681 pi-Stacking: A:F.625, A:F.625 pi-Cation interactions: A:K.649

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 9 residues within 4Å: Chain A: D.508, K.509, T.510, T.745, G.746, K.854, N.876 Ligands: ADP.1, MG.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.508

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.508, T.510, G.511, D.873 Ligands: ALF.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.508, A:T.510, A:D.873 MG.4: 2 residues within 4Å: Chain A: R.681 Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 14 residues within 4Å: Chain A: I.264, L.268, Y.271, V.474, L.477, Y.478, S.481, R.484, L.963, V.964, T.967, T.968, V.971 Ligands: Y01.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.264, A:L.268, A:V.474, A:Y.478, A:L.963 Hydrogen bonds: A:S.481, A:S.481 Salt bridges: A:K.275, A:R.484 Y01.6: 12 residues within 4Å: Chain A: V.964, T.968, L.972, R.975, P.1075, V.1078, A.1079, L.1082, L.1083, V.1086, L.1097 Ligands: Y01.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.972, A:L.1082, A:L.1097 Salt bridges: A:R.975

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sim, S.I. et al., Structural basis of polyamine transport by human ATP13A2 (PARK9). Mol.Cell (2021)

Release Date

2021-11-10

Peptides

Isoform 3 of Polyamine-transporting ATPase 13A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Isoform 3 of Polyamine-transporting ATPase 13A2

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