SMTL ID : 9j53.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

PC1.1: 20 residues within 4Å: Chain A: L.278, L.285, H.299, L.305, N.306, S.309, N.310, L.311, L.323, M.355, V.356, L.359, K.369, S.370, W.373, L.374, W.395, Q.399, I.406, L.410 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.278, A:L.285, A:L.323, A:V.356, A:L.359, A:W.373, A:W.395, A:W.395, A:I.406 Hydrogen bonds: A:S.309, A:L.311 Salt bridges: A:H.299 PC1.2: 12 residues within 4Å: Chain A: V.237, C.241, F.244, F.276, F.283, I.287, Y.290, H.313, Q.314, F.317 Chain B: W.232, F.235 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.237, A:F.244, A:F.244, A:F.244, A:F.276, A:F.283, A:F.283, A:F.283, A:I.287, A:Q.314, A:F.317, B:F.235, B:F.235 Hydrogen bonds: A:Q.314 PC1.4: 19 residues within 4Å: Chain B: L.278, F.281, L.285, L.305, N.306, S.309, N.310, L.311, Y.352, M.355, V.356, F.358, L.359, K.369, S.370, W.373, L.374, W.395, L.396 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.281, B:L.285, B:L.311, B:Y.352, B:V.356, B:F.358, B:L.359, B:L.359, B:W.373, B:W.373, B:L.374, B:W.395, B:L.396 Salt bridges: B:E.304, B:K.369 PC1.5: 14 residues within 4Å: Chain A: A.231, W.232, F.235 Chain B: V.237, C.241, F.244, F.276, I.279, F.283, I.287, Y.290, H.313, Q.314, F.317 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.237, B:F.244, B:F.244, B:F.276, B:I.279, B:F.283, B:F.283, B:F.283, B:F.283, B:I.287, B:Y.290, B:Y.290, B:F.317, A:F.235, A:F.235 Hydrogen bonds: B:Q.314

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

PO4.3: 8 residues within 4Å: Chain A: N.401, S.404, Q.452, P.455, A.456, T.486, W.573, I.577 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.401, A:N.401, A:N.401, A:S.404, A:Q.452 PO4.6: 8 residues within 4Å: Chain B: N.401, S.404, Q.452, P.455, A.456, T.486, W.573, I.577 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.404, B:Q.452, B:Q.452

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
B

B
A

Membrane

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

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