SMTL ID : 9dvl.1

Structure of the phosphate exporter XPR1/SLC53A1, InsP6-supplemented

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.97 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: V.389, F.394, R.459, Q.462, C.463, R.466, H.476, N.479, F.623 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.479 Salt bridges: A:R.459, A:R.466 PO4.2: 8 residues within 4Å: Chain A: D.398, N.401, S.402, R.570, W.573, E.600, R.603, R.604 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.402, A:S.402, A:E.600 Salt bridges: A:R.570, A:R.603, A:R.604 PO4.3: 9 residues within 4Å: Chain A: R.270, H.441, I.579, T.580, T.582, L.585, P.586, G.589, D.590 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.582, A:D.590, A:D.590 Salt bridges: A:R.270, A:H.441 PO4.6: 9 residues within 4Å: Chain B: V.389, F.394, R.459, Q.462, C.463, R.466, H.476, N.479, F.623 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.479 Salt bridges: B:R.459, B:R.466 PO4.7: 9 residues within 4Å: Chain B: D.398, N.401, K.482, Y.483, T.525, R.570, W.573, R.603, R.604 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.401, B:R.603 Salt bridges: B:R.570, B:R.604 PO4.8: 6 residues within 4Å: Chain B: R.270, M.408, E.411, Y.412, R.448, T.580 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.412 Salt bridges: B:R.270, B:R.448

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 16 residues within 4Å: Chain A: I.287, Y.290, G.291, Q.294, Y.553, P.554, Y.558, C.561, A.562, I.564, E.565, F.602, F.605, V.606, F.609, F.610 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.558, A:E.565, A:F.602, A:F.605, A:V.606, A:F.609, A:F.609, A:F.610 CLR.9: 14 residues within 4Å: Chain B: I.287, G.291, Q.294, Y.553, P.554, Y.558, C.561, A.562, E.565, F.602, F.605, V.606, F.609, F.610 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.553, B:E.565, B:F.602, B:F.605, B:V.606, B:F.609, B:F.609, B:F.610

2 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.5: 34 residues within 4Å: Chain A: L.278, F.281, L.282, L.285, T.289, W.292, H.299, F.303, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, Y.352, M.355, V.356, F.358, L.359, K.369, S.370, R.371, W.373, L.374, L.377, L.378, W.395, L.396, L.400, L.403, I.406, L.407 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.278, A:L.278, A:L.282, A:F.303, A:F.303, A:L.311, A:L.316, A:I.319, A:M.355, A:F.358, A:W.373, A:L.374, A:L.374, A:W.395, A:W.395, A:L.396 Hydrogen bonds: A:T.289, A:S.309, A:L.311 Salt bridges: A:H.299 CPL.10: 35 residues within 4Å: Chain B: L.278, F.281, L.282, L.285, T.289, W.292, H.299, F.303, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, Y.352, M.355, V.356, F.358, L.359, K.369, S.370, R.371, W.373, L.374, L.378, W.395, L.396, Q.399, L.400, L.403, I.406, L.407, L.410 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.278, B:F.281, B:L.285, B:F.303, B:L.305, B:L.311, B:L.316, B:V.356, B:F.358, B:L.359, B:W.373, B:L.374, B:W.395, B:I.406, B:L.407 Hydrogen bonds: B:L.311 Salt bridges: B:H.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Q. et al., Transport and InsP 8 gating mechanisms of the human inorganic phosphate exporter XPR1. Nat Commun (2025)

Release Date

2025-04-02

Peptides

Solute carrier family 53 member 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Solute carrier family 53 member 1

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