SMTL ID : 9iuc.1

Cryo-EM structure of human XPR1 in complex with InsP6 in closed state - in the presence of KIDINS220-1-432 without substrate KH2PO4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 6 residues within 4Å: Chain A: Y.558, C.561, E.565, F.605, V.606, F.609 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.558, A:E.565, A:F.605, A:V.606, A:F.609, A:F.609 CLR.4: 10 residues within 4Å: Chain A: Y.445, A.449, I.450, C.453, W.457, F.460, F.487, T.491, A.494, L.495 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.449, A:I.450, A:F.460, A:F.487, A:T.491, A:A.494 CLR.5: 4 residues within 4Å: Chain A: L.407, E.411, I.414, I.454 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.407, A:E.411, A:I.454 CLR.6: 4 residues within 4Å: Chain A: L.329, P.338 Chain B: L.253 Ligands: 3PE.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.329, A:P.338, B:L.253 CLR.7: 2 residues within 4Å: Chain A: I.519, F.571 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.519, A:F.571, A:F.571 CLR.10: 7 residues within 4Å: Chain A: V.356, L.410, M.413, I.414, Y.417, S.418, W.423 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.356, A:L.410, A:I.414, A:Y.417, A:W.423 CLR.14: 4 residues within 4Å: Chain A: L.253, F.257 Chain B: P.338 Ligands: 3PE.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.253, A:F.257 CLR.16: 5 residues within 4Å: Chain B: Y.558, E.565, F.605, V.606, F.609 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.558, B:E.565, B:F.605, B:V.606, B:F.609 CLR.19: 8 residues within 4Å: Chain B: Y.445, A.449, W.457, F.460, F.487, T.491, A.494, L.495 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.449, B:F.460, B:F.487, B:T.491, B:A.494 CLR.20: 4 residues within 4Å: Chain B: L.407, E.411, I.414, I.454 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.407, B:E.411, B:E.411, B:I.454 CLR.21: 1 residues within 4Å: Chain B: F.571 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.571 CLR.24: 7 residues within 4Å: Chain B: V.356, L.410, M.413, I.414, Y.417, S.418, W.423 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.356, B:L.410, B:I.414, B:W.423

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 8 residues within 4Å: Chain A: M.1, K.2, F.3, K.158, K.162, K.165, Y.368, K.369 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:M.1, A:K.2 Salt bridges: A:K.2, A:K.2, A:K.158, A:K.162, A:K.165, A:K.369 IHP.17: 7 residues within 4Å: Chain B: M.1, K.2, F.3, K.162, K.364, Y.368, K.369 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:M.1, B:K.2 Salt bridges: B:K.2, B:K.2, B:K.162, B:K.165, B:K.364, B:K.369, B:K.369

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.3: 19 residues within 4Å: Chain A: L.278, F.281, L.285, T.289, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, Y.352, L.359, S.370, W.373, L.374, W.395, L.400 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.278, A:L.278, A:L.285, A:I.319, A:L.323, A:Y.352, A:L.374, A:L.374, A:L.374, A:W.395, A:W.395, A:L.400 Hydrogen bonds: A:S.309, A:S.370 3PE.8: 16 residues within 4Å: Chain A: Q.227, P.228, A.229, C.241, F.244, I.245, I.249, F.283, I.287, Y.290, R.293, H.313, Q.314 Chain B: A.231, W.232 Ligands: PLM.12 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.244, A:I.245, A:I.249, A:F.283, A:F.283, A:I.287, A:Y.290 Hydrogen bonds: A:Q.227, A:A.229, A:Q.314 Salt bridges: A:H.313 3PE.13: 16 residues within 4Å: Chain A: I.245, V.246, T.250, L.253, F.257, K.258 Chain B: I.243, L.247, K.258, L.329, L.332, A.333, F.336, P.338 Ligands: CLR.14, 3PE.15 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.245, A:V.246, A:L.253, A:F.257, B:I.243, B:I.243, B:L.247, B:L.332, B:A.333, B:F.336, B:P.338 Salt bridges: A:K.258 3PE.15: 15 residues within 4Å: Chain A: I.243, T.250, L.329, L.332, A.333, F.336, P.338 Chain B: V.246, I.249, T.250, L.253, F.257, K.258 Ligands: CLR.6, 3PE.13 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.246, B:V.246, B:I.249, B:L.253, B:F.257, B:K.258, A:I.243, A:T.250, A:L.329, A:L.332, A:A.333, A:F.336, A:P.338 Salt bridges: B:K.258, B:K.258 3PE.18: 20 residues within 4Å: Chain B: L.278, F.281, L.285, T.289, L.305, N.306, S.309, N.310, L.311, L.316, I.319, L.323, Y.352, M.355, L.359, S.370, W.373, L.374, W.395, L.400 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.278, B:L.285, B:I.319, B:L.323, B:Y.352, B:M.355, B:L.359, B:L.374, B:L.374, B:W.395, B:W.395 Hydrogen bonds: B:S.309, B:S.370, B:S.370 3PE.22: 13 residues within 4Å: Chain A: A.231, W.232 Chain B: P.228, A.229, C.241, F.244, N.248, F.283, Y.290, R.293, H.313, Q.314 Ligands: PLM.26 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.244, B:N.248, B:F.283, B:Y.290, A:W.232, A:W.232 Hydrogen bonds: B:Q.227, B:A.229, B:Q.314 Salt bridges: B:H.313

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.9: 4 residues within 4Å: Chain A: W.232, F.235, R.236 Chain B: I.245 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.235, B:I.245 Salt bridges: A:R.236 PLM.12: 4 residues within 4Å: Chain A: E.280, Y.290 Ligands: 3PE.8, ACD.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.290 PLM.23: 5 residues within 4Å: Chain B: W.232, T.233, F.235, R.236, L.239 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.232, B:F.235, B:L.239 Salt bridges: B:R.236 PLM.26: 3 residues within 4Å: Chain B: Y.290 Ligands: 3PE.22, ACD.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.290

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.11: 4 residues within 4Å: Chain A: W.266, F.276, I.591 Ligands: PLM.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.266, A:W.266, A:I.591 ACD.25: 4 residues within 4Å: Chain B: W.266, F.276, I.591 Ligands: PLM.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.266, B:F.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zuo, P. et al., Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate. 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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