SMTL ID : 9j52.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

PC1.1: 25 residues within 4Å: Chain A: G.274, L.278, F.281, L.282, L.285, L.305, N.306, S.309, N.310, L.311, I.319, Y.352, M.355, L.359, K.369, S.370, W.373, L.374, L.378, W.395, L.396, L.400, I.406, D.409, L.410 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.278, A:F.281, A:L.282, A:L.282, A:L.285, A:I.319, A:Y.352, A:L.359, A:L.359, A:L.374, A:L.374, A:L.378, A:W.395, A:L.396, A:L.400, A:L.400, A:I.406, A:D.409, A:L.410 Hydrogen bonds: A:L.311 PC1.2: 12 residues within 4Å: Chain A: V.237, C.241, F.244, I.279, F.283, Y.290, R.293, Q.314, F.317 Chain B: A.231, W.232, F.235 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.237, A:F.244, A:F.244, A:I.279, A:F.283, A:F.283, A:F.283, A:F.283, A:F.283, A:Y.290, A:Y.290, A:Y.290, A:F.317, B:F.235, B:F.235 Hydrogen bonds: A:Q.314 Salt bridges: A:R.293, A:H.313 PC1.4: 19 residues within 4Å: Chain B: L.278, F.281, L.285, T.289, H.299, L.305, N.306, S.309, N.310, L.311, Y.352, L.359, K.369, S.370, W.373, L.374, W.395, I.406, L.410 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.278, B:L.278, B:F.281, B:L.285, B:Y.352, B:L.359, B:L.359, B:W.373, B:W.395, B:W.395, B:I.406, B:L.410 Hydrogen bonds: B:N.310, B:L.311 Salt bridges: B:H.299 PC1.5: 13 residues within 4Å: Chain A: A.231, W.232, F.235 Chain B: V.237, C.241, F.244, I.279, E.280, F.283, Y.290, H.313, Q.314, F.317 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.237, B:F.244, B:F.244, B:I.279, B:E.280, B:F.283, B:F.283, B:F.283, B:Y.290, B:Y.290, B:F.317, A:W.232, A:F.235, A:F.235 Hydrogen bonds: B:Y.290, B:Q.314 Salt bridges: B:H.313

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

PO4.3: 9 residues within 4Å: Chain A: D.398, N.401, S.402, K.482, Y.483, T.525, R.570, R.603, R.604 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.482, A:R.570, A:R.603, 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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