SMTL ID : 7m5v.1

human ATP13A2 in the AMPPNP-bound occluded state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.513, T.515, G.516, D.878, N.881 Ligands: ANP.23 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.513, A:T.515, A:T.515

4 x 1DO: 1-DODECANOL(Non-covalent)

1DO.2: 17 residues within 4Å: Chain A: Y.422, S.425, F.428, V.429, L.432, V.468, V.469, P.470, L.473, M.477, F.934, M.937, A.938, S.941, L.942, L.996 Ligands: LMT.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.432, A:L.473, A:F.934, A:F.934, A:L.996 1DO.8: 6 residues within 4Å: Chain A: W.258, L.961, L.964, G.1104, P.1105 Ligands: 1DO.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.258, A:W.258, A:W.258, A:L.961, A:L.961 1DO.9: 10 residues within 4Å: Chain A: L.961, L.964, A.965, V.969, V.1091, L.1102, P.1105, L.1106 Ligands: 1DO.8, Y01.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.965, A:V.969, A:V.969 1DO.17: 11 residues within 4Å: Chain A: Y.442, I.946, L.949, I.950, T.953, I.954, T.1013, L.1017, Y.1020, F.1021, L.1024 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.953, A:Y.1020

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

LMT.3: 19 residues within 4Å: Chain A: N.238, Y.240, Y.241, S.274, V.429, L.432, S.433, A.436, L.437, T.440, V.465, V.468, V.469, L.473, P.474, M.477, T.478 Ligands: 1DO.2, Y01.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.436, A:L.437, A:V.465, A:V.468 Hydrogen bonds: A:N.238, A:Y.241, A:Y.241

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 12 residues within 4Å: Chain A: N.238, P.239, Y.240, F.243, S.433, L.437, L.462, V.465, V.469 Ligands: LMT.3, Y01.5, D10.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.243, A:F.243 Y01.5: 11 residues within 4Å: Chain A: A.58, G.59, P.61, L.237, N.238, P.239, G.242, F.243, F.246, L.462 Ligands: Y01.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.61, A:L.237, A:P.239, A:F.246 Y01.10: 16 residues within 4Å: Chain A: I.269, L.273, Y.276, K.280, V.479, L.482, Y.483, S.486, R.489, L.968, V.969, T.972, T.973, V.976, L.977 Ligands: Y01.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.273, A:Y.483 Salt bridges: A:K.280 Y01.11: 14 residues within 4Å: Chain A: Y.483, V.969, T.973, L.977, R.980, P.1080, V.1083, A.1084, L.1087, L.1088, L.1102 Ligands: 1DO.9, Y01.10, D12.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.969, A:A.1084, A:L.1087, A:L.1087, A:L.1088 Hydrogen bonds: A:R.980

9 x D10: DECANE(Non-functional Binders)(Non-covalent)

D10.6: 4 residues within 4Å: Chain A: L.62, F.65, P.239 Ligands: Y01.4 No protein-ligand interaction detected (PLIP) D10.13: 5 residues within 4Å: Chain A: V.1079, V.1083, L.1087 Ligands: D12.12, D10.14 No protein-ligand interaction detected (PLIP) D10.14: 7 residues within 4Å: Chain A: Y.1076, T.1077, V.1079, L.1082, V.1083 Ligands: D10.13, D10.16 No protein-ligand interaction detected (PLIP) D10.15: 10 residues within 4Å: Chain A: A.1063, P.1074, L.1075, Y.1076, L.1082, L.1085, F.1128, F.1132 Ligands: D10.16, D10.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1076 D10.16: 4 residues within 4Å: Chain A: Y.1076, L.1082 Ligands: D10.14, D10.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1076 D10.19: 5 residues within 4Å: Chain A: L.1118, L.1121, G.1122, T.1125 Ligands: D10.20 No protein-ligand interaction detected (PLIP) D10.20: 3 residues within 4Å: Chain A: L.1097, L.1118 Ligands: D10.19 No protein-ligand interaction detected (PLIP) D10.21: 6 residues within 4Å: Chain A: V.1093, G.1094, L.1097, V.1098, P.1099, T.1114 No protein-ligand interaction detected (PLIP) D10.22: 6 residues within 4Å: Chain A: T.1125, F.1128, V.1129, F.1132, M.1133 Ligands: D10.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1128

2 x D12: DODECANE(Non-covalent)

D12.7: 7 residues within 4Å: Chain A: I.248, L.252, Y.257, W.258, A.260, L.261, F.264 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.257, A:W.258, A:W.258 D12.12: 7 residues within 4Å: Chain A: R.980, V.1079, P.1080, V.1083, L.1087 Ligands: Y01.11, D10.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1079

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.18: 3 residues within 4Å: Chain A: N.1033, T.1035, V.1036 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.1035, A:T.1035

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.23: 26 residues within 4Å: Chain A: D.513, K.514, T.515, D.571, M.573, D.574, F.630, S.632, Q.635, R.636, M.637, K.654, G.655, S.656, P.657, R.686, V.687, V.688, V.749, T.750, G.751, D.752, R.853, K.859, N.881 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.513, A:K.514, A:T.515, A:T.515, A:D.574, A:K.654, A:K.654, A:R.686, A:R.686, A:V.749, A:G.751, A:D.752, A:R.853, A:K.859, A:N.881 pi-Stacking: A:F.630, A:F.630

1 x EUJ: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate(Non-covalent)

EUJ.24: 12 residues within 4Å: Chain A: K.420, H.424, K.427, G.994, A.995, L.997, R.1150, K.1152, A.1154, K.1156, K.1157, K.1160 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.1150, A:K.1157 Salt bridges: A:K.420, A:H.424, A:R.1150, A:K.1152, A:K.1152, A:K.1157, A:K.1160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tillinghast, J. et al., Structural mechanisms for gating and ion selectivity of the human polyamine transporter ATP13A2. Mol.Cell (2021)

Release Date

2022-03-30

Peptides

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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Polyamine-transporting ATPase 13A2