SMTL ID : 9j51.1

CryoEM structure of human XPR1 in complex with phosphate in state A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

PC1.1: 20 residues within 4Å: Chain A: L.278, F.281, L.285, H.299, L.305, N.306, S.309, N.310, L.311, L.323, Y.352, V.356, F.358, K.369, S.370, W.373, L.374, F.382, W.395, L.410 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.278, A:F.281, A:L.285, A:L.285, A:L.311, A:L.323, A:V.356, A:F.358, A:F.358, A:L.374, A:F.382, A:W.395 Hydrogen bonds: A:L.311 PC1.2: 16 residues within 4Å: Chain A: T.234, V.237, C.241, F.244, F.276, I.279, F.283, Y.290, Q.294, H.313, Q.314, F.317, G.321 Chain B: A.231, W.232, F.235 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.237, A:F.276, A:I.279, A:F.283, A:F.283, A:F.283, A:F.283, A:F.283, A:Y.290, A:F.317, A:F.317, B:W.232 Hydrogen bonds: A:Q.314 Salt bridges: A:H.313 PC1.4: 22 residues within 4Å: Chain B: L.278, F.281, L.282, L.285, T.289, H.299, F.303, L.305, N.306, S.309, N.310, L.311, I.319, M.355, V.356, L.359, K.369, S.370, W.373, L.374, W.395, L.400 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.278, B:L.278, B:F.281, B:L.282, B:L.285, B:F.303, B:L.311, B:I.319, B:V.356, B:L.359, B:L.374, B:W.395, B:W.395, B:L.400 Hydrogen bonds: B:T.289, B:S.309, B:L.311 Salt bridges: B:H.299 PC1.5: 17 residues within 4Å: Chain A: A.231, W.232, F.235 Chain B: T.234, C.241, F.244, F.276, I.279, E.280, F.283, I.287, Y.290, R.293, Q.294, H.313, Q.314, F.317 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.276, B:I.279, B:E.280, B:E.280, B:F.283, B:F.283, B:F.283, B:F.283, B:I.287, B:Y.290, B:F.317, B:F.317, B:F.317, A:F.235, A:F.235 Salt bridges: B:R.293, B:H.313

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

PO4.3: 8 residues within 4Å: Chain A: D.398, K.482, Y.483, D.529, D.533, R.570, R.604, W.607 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.483, A:T.525, A:D.533 Salt bridges: A:K.482, A:R.570, A:R.604

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., Structural insights into the mechanism of phosphate recognition and transport by XPR1. Nat Commun (2025)

Release Date

2025-01-15

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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