SMTL ID : 7n74.1

Cryo-EM structure of ATP13A2 D508N mutant in the E1-ATP-like state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 24 residues within 4Å: Chain A: N.508, K.509, T.510, D.566, M.568, D.569, F.625, S.627, Q.630, M.632, K.649, G.650, S.651, R.681, V.682, V.683, V.744, T.745, G.746, D.747, R.848, K.854, N.876 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.508, A:K.509, A:T.510, A:T.510, A:D.566, A:D.566, A:S.627, A:K.649, A:K.649, A:R.681, A:V.682, A:T.745, A:G.746, A:D.747, A:D.747, A:R.848, A:R.848, A:N.876 Salt bridges: A:K.854, A:K.854 pi-Stacking: A:F.625

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.873 Ligands: ATP.1 No protein-ligand interaction detected (PLIP)

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 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: Y01.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.264, A:I.264, A:L.268, A:T.968 Hydrogen bonds: A:Y.271 Salt bridges: A:R.484 Y01.4: 13 residues within 4Å: Chain A: Y.478, V.964, T.968, L.972, R.975, P.1075, V.1078, A.1079, L.1082, L.1083, V.1086, L.1097 Ligands: Y01.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.964, A:T.968, A:A.1079, A:L.1082, A:V.1086, 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