SMTL ID : 7n78.1

Cryo-EM structure of ATP13A2 in the E2-Pi state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 11 residues within 4Å: Chain A: T.341, G.342, E.343, D.508, K.509, T.510, T.745, G.746, K.854, N.876 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.508, A:K.509, A:T.510, A:T.510, A:T.510, A:T.745, A:G.746, A:N.876 Salt bridges: A:K.854

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.508, T.510, D.873 Ligands: PO4.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.508, A:T.510, A:D.873

1 x SPM: SPERMINE(Non-covalent)

SPM.3: 17 residues within 4Å: Chain A: W.246, D.249, H.250, Y.251, Y.254, R.455, D.458, T.461, V.462, Y.935, Q.939, N.952, G.954, D.955, F.958, D.962, P.1034 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.246, A:V.462, A:F.958 Hydrogen bonds: A:W.246, A:D.955, A:D.962

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 14 residues within 4Å: Chain A: Y.478, L.956, L.959, L.963, V.964, T.967, T.968, V.971, L.972, R.975 Ligands: Y01.5, LMT.7, LMT.8, LMT.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.959, A:L.963, A:V.964, A:T.967, A:T.968 Salt bridges: A:R.975 Y01.5: 14 residues within 4Å: Chain A: C.257, I.261, V.474, L.477, Y.478, S.481, R.482, R.485, L.963, T.967, V.971 Ligands: Y01.4, PC1.6, LMT.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.261, A:L.477, A:L.477, A:R.482, A:T.967 Hydrogen bonds: A:S.481 Salt bridges: A:R.485 Y01.11: 14 residues within 4Å: Chain A: A.1058, G.1063, P.1069, L.1070, Y.1071, L.1077, L.1080, A.1081, S.1084, S.1085, V.1088, F.1123, F.1127 Ligands: PC1.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1077 Hydrogen bonds: A:L.1070, A:Y.1071

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.6: 18 residues within 4Å: Chain A: I.261, I.264, S.265, L.268, S.269, K.272, A.467, A.470, A.471, T.473, V.474, L.477, M.932, T.966, T.967, A.970, V.971 Ligands: Y01.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.470, A:A.471 Hydrogen bonds: A:S.269 PC1.10: 12 residues within 4Å: Chain A: F.1051, L.1054, I.1055, S.1084, V.1088, L.1092, L.1113, L.1116, V.1119, T.1120, F.1123 Ligands: Y01.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1051, A:I.1055, A:V.1088, A:L.1092, A:L.1116, A:F.1123

3 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.7: 13 residues within 4Å: Chain A: L.956, A.960, V.964, I.965, L.1083, V.1086, L.1087, L.1097, G.1099, P.1100, L.1101 Ligands: Y01.4, LMT.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.956, A:V.964, A:V.1086, A:L.1097, A:L.1097, A:P.1100 Hydrogen bonds: A:G.1099 LMT.8: 9 residues within 4Å: Chain A: W.253, L.256, C.257, L.956, L.959, L.963 Ligands: Y01.4, Y01.5, LMT.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.253, A:L.256, A:L.956, A:L.959 LMT.9: 9 residues within 4Å: Chain A: T.968, L.972, V.1074, P.1075, V.1078, A.1079, L.1082, L.1083 Ligands: Y01.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1074, A:V.1078

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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