SMTL ID : 7m5x.1

Human ATP13A2 in the outward-facing E2 state bound to spermine and beryllium fluoride

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: D.513, T.515, G.516, T.517, D.878, G.879 Ligands: BEF.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.513, A:T.515, A:D.878, H2O.1

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 12 residues within 4Å: Chain A: T.346, G.347, E.348, D.513, K.514, T.515, T.750, G.751, D.752, K.859, N.881 Ligands: MG.1 No protein-ligand interaction detected (PLIP)

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 16 residues within 4Å: Chain A: C.262, I.266, V.479, L.482, Y.483, S.486, R.487, R.490, L.968, T.972, V.976 Ligands: LMT.4, Y01.5, CLR.7, D10.11, D10.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.266, A:Y.483, A:Y.483, A:T.972 Y01.5: 17 residues within 4Å: Chain A: Y.483, L.961, L.964, A.965, L.968, V.969, T.972, T.973, V.976, L.977, R.980 Ligands: Y01.3, D10.9, D10.10, D10.11, C14.15, D12.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.972, A:V.976 Salt bridges: A:R.980 Y01.8: 13 residues within 4Å: Chain A: S.227, Y.228, P.229, L.232, Y.241, Q.244, A.245, I.248, F.264, S.267, S.268, I.271, C.272 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.228, A:F.264, A:I.271 Hydrogen bonds: A:Y.228 Salt bridges: A:R.279

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

LMT.4: 25 residues within 4Å: Chain A: Y.241, Y.259, I.266, S.270, L.273, S.274, K.277, T.278, A.472, A.475, A.476, T.478, V.479, L.482, I.496, H.497, P.498, L.499, M.937, T.971, T.972, A.975, V.976 Ligands: Y01.3, CLR.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.266, A:A.472, A:A.475, A:A.475 Hydrogen bonds: A:K.277, A:H.497

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 12 residues within 4Å: Chain A: A.1063, L.1075, Y.1076, L.1082, L.1085, A.1086, S.1089, S.1090, F.1128, F.1132 Ligands: D10.19, D10.20 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1075, A:L.1075, A:Y.1076, A:L.1082, A:L.1082, A:L.1085, A:A.1086, A:F.1132 CLR.7: 12 residues within 4Å: Chain A: L.261, C.262, L.265, I.266, I.269, L.273, L.482 Ligands: Y01.3, LMT.4, D10.12, D10.13, D12.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.261, A:L.265, A:I.266, A:I.269 CLR.21: 13 residues within 4Å: Chain A: N.238, P.239, Y.240, F.243, K.427, V.429, S.433, A.436, L.437, V.465, V.469 Ligands: D10.17, CLR.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.239, A:Y.240, A:F.243, A:V.429 CLR.22: 7 residues within 4Å: Chain A: P.239, G.242, F.243, F.246, L.462 Ligands: D10.17, CLR.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.239

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

D10.9: 8 residues within 4Å: Chain A: L.977, V.1079, P.1080, V.1083, A.1084, L.1087 Ligands: Y01.5, D10.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1083, A:L.1087 D10.10: 5 residues within 4Å: Chain A: R.980, P.1080 Ligands: Y01.5, D10.9, D10.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.1080 D10.11: 4 residues within 4Å: Ligands: Y01.3, Y01.5, D10.10, D10.13 No protein-ligand interaction detected (PLIP) D10.12: 5 residues within 4Å: Chain A: I.269, L.273 Ligands: CLR.7, D10.13, D10.14 No protein-ligand interaction detected (PLIP) D10.13: 4 residues within 4Å: Ligands: Y01.3, CLR.7, D10.11, D10.12 No protein-ligand interaction detected (PLIP) D10.14: 4 residues within 4Å: Chain A: C.272, L.273, Y.276 Ligands: D10.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.276 D10.17: 4 residues within 4Å: Chain A: P.239, V.429 Ligands: CLR.21, CLR.22 No protein-ligand interaction detected (PLIP) D10.18: 7 residues within 4Å: Chain A: G.1115, L.1118, L.1119, L.1121, G.1122, T.1125 Ligands: D10.20 No protein-ligand interaction detected (PLIP) D10.19: 6 residues within 4Å: Chain A: F.1128, V.1129, F.1132, M.1133, S.1136 Ligands: CLR.6 No protein-ligand interaction detected (PLIP) D10.20: 10 residues within 4Å: Chain A: F.1056, I.1060, S.1089, V.1093, L.1121, V.1124, T.1125, F.1128 Ligands: CLR.6, D10.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1121, A:F.1128, A:F.1128

1 x C14: TETRADECANE(Non-covalent)

C14.15: 12 residues within 4Å: Chain A: L.961, A.965, V.969, L.1088, V.1091, L.1092, L.1095, L.1102, P.1105, L.1106 Ligands: Y01.5, D12.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.961, A:L.1106

1 x D12: DODECANE(Non-covalent)

D12.16: 7 residues within 4Å: Chain A: W.258, L.961, L.964, L.968 Ligands: Y01.5, CLR.7, C14.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.258, A:W.258, A:L.968

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

NAG.23: 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 SPK: SPERMINE (FULLY PROTONATED FORM)(Non-covalent)

SPK.24: 16 residues within 4Å: Chain A: W.251, D.254, H.255, Y.256, Y.259, R.460, D.463, T.466, V.467, Y.940, Q.944, N.957, D.960, F.963, D.967, P.1039 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.467, A:F.963, A:F.963 Hydrogen bonds: A:D.463, A:Q.944, A:D.960, A:D.967 Water bridges: A:Y.940

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.25: 16 residues within 4Å: Chain A: P.993, G.994, A.995, L.997, S.998, V.999, P.1000, L.1002, L.1146, L.1149, R.1150, R.1153, S.1155, K.1156, K.1157, K.1160 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.999, A:L.1002 Hydrogen bonds: A:G.994, A:A.995, A:V.999, A:R.1153, A:S.1155, A:S.1155 Salt bridges: A:R.1153, 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

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