SMTL ID : 8x5f.1

human XPR1 in complex with InsP6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.96 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: N.401, K.482, Y.483, T.525, R.570, W.573, R.604 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.401, A:N.401, A:R.604 Salt bridges: A:K.482, A:R.570 PO4.2: 5 residues within 4Å: Chain A: P.475, W.528, M.532, D.533, R.611 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.533 Salt bridges: A:R.611 PO4.3: 5 residues within 4Å: Chain A: R.270, R.273, D.409, Y.412, R.448 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.409, A:D.409 Salt bridges: A:R.270, A:R.273, A:R.448 PO4.4: 7 residues within 4Å: Chain A: V.389, F.394, R.459, Q.462, C.463, R.466, H.476 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.462 Salt bridges: A:R.459, A:R.466 PO4.23: 8 residues within 4Å: Chain B: 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:R.603 Salt bridges: B:K.482, B:R.570, B:R.604 PO4.24: 4 residues within 4Å: Chain B: W.528, M.532, D.533, R.611 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.479 Salt bridges: B:R.611 PO4.25: 6 residues within 4Å: Chain B: F.394, R.459, Q.462, C.463, R.466, N.479 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.462, B:N.479 Salt bridges: B:R.459, B:R.466 PO4.26: 6 residues within 4Å: Chain B: R.270, R.273, M.408, D.409, Y.412, R.448 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.409, B:D.409 Salt bridges: B:R.270, B:R.273, B:R.448

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.5: 12 residues within 4Å: Chain A: M.1, K.2, F.3, Y.22, Y.30, K.158, K.161, K.162, K.165 Chain B: R.211, M.215, R.219 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.1, A:K.2, A:F.3, A:Y.30 Water bridges: A:K.26, A:K.26 Salt bridges: A:K.2, A:K.158, A:K.161, A:K.161, A:K.161, A:K.162, A:K.162, A:K.162, A:K.165, A:K.165, A:K.165, B:R.211, B:R.219 IHP.27: 12 residues within 4Å: Chain A: R.211, M.215, R.219 Chain B: M.1, K.2, F.3, Y.22, Y.30, K.158, K.161, K.162, K.165 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.1, B:K.2, B:F.3, B:Y.30 Water bridges: B:K.162 Salt bridges: B:K.2, B:K.158, B:K.161, B:K.161, B:K.161, B:K.162, B:K.162, B:K.162, B:K.165, B:K.165, B:K.165, A:R.211, A:R.219

30 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)(Non-functional Binders)

POV.6: 3 residues within 4Å: Chain A: W.232, R.236 Ligands: POV.20 Ligand excluded by PLIP POV.7: 4 residues within 4Å: Chain A: S.330, A.333, P.338 Ligands: POV.28 Ligand excluded by PLIP POV.8: 2 residues within 4Å: Ligands: POV.17, POV.22 Ligand excluded by PLIP POV.10: 2 residues within 4Å: Chain A: F.474, Y.524 Ligand excluded by PLIP POV.11: 4 residues within 4Å: Chain A: I.450, C.453, I.454, T.491 Ligand excluded by PLIP POV.12: 2 residues within 4Å: Chain A: C.561, I.564 Ligand excluded by PLIP POV.13: 3 residues within 4Å: Chain A: W.266, I.591 Ligands: POV.14 Ligand excluded by PLIP POV.14: 8 residues within 4Å: Chain A: A.255, I.265, I.269, R.273, F.276, L.331 Ligands: POV.13, POV.16 Ligand excluded by PLIP POV.15: 1 residues within 4Å: Chain A: W.423 Ligand excluded by PLIP POV.16: 4 residues within 4Å: Chain A: N.248, L.251, V.256 Ligands: POV.14 Ligand excluded by PLIP POV.17: 3 residues within 4Å: Chain A: F.602 Ligands: POV.8, CLR.9 Ligand excluded by PLIP POV.18: 6 residues within 4Å: Chain A: T.250, L.253, F.257 Chain B: T.250, L.332 Ligands: POV.30 Ligand excluded by PLIP POV.19: 15 residues within 4Å: Chain A: L.285, L.305, N.306, S.309, N.310, L.311, Y.352, M.355, K.369, S.370, W.373, L.374, W.395, L.400, I.406 Ligand excluded by PLIP POV.20: 6 residues within 4Å: Chain A: R.236, E.318, F.322, F.366, Y.367 Ligands: POV.6 Ligand excluded by PLIP POV.21: 12 residues within 4Å: Chain A: A.231, W.232 Chain B: C.241, F.244, F.276, I.279, F.283, Y.290, Q.314, F.317, G.321 Ligands: POV.31 Ligand excluded by PLIP POV.22: 10 residues within 4Å: Chain A: C.241, F.276, I.279, F.283, Y.290, Q.314, F.317 Chain B: A.231, W.232 Ligands: POV.8 Ligand excluded by PLIP POV.28: 4 residues within 4Å: Chain A: T.250 Chain B: T.250, L.253 Ligands: POV.7 Ligand excluded by PLIP POV.29: 4 residues within 4Å: Chain B: W.232, R.236, L.239 Ligands: POV.42 Ligand excluded by PLIP POV.30: 3 residues within 4Å: Chain B: A.333, P.338 Ligands: POV.18 Ligand excluded by PLIP POV.31: 4 residues within 4Å: Chain B: Y.290, F.602 Ligands: POV.21, POV.37 Ligand excluded by PLIP POV.33: 2 residues within 4Å: Chain B: I.450, T.491 Ligand excluded by PLIP POV.34: 8 residues within 4Å: Chain B: A.255, I.265, I.269, R.273, F.276, F.335 Ligands: POV.35, POV.38 Ligand excluded by PLIP POV.35: 5 residues within 4Å: Chain B: N.248, L.251, V.256, F.276 Ligands: POV.34 Ligand excluded by PLIP POV.36: 1 residues within 4Å: Chain B: Y.524 Ligand excluded by PLIP POV.37: 3 residues within 4Å: Chain B: F.602 Ligands: POV.31, CLR.32 Ligand excluded by PLIP POV.38: 3 residues within 4Å: Chain B: I.265, I.591 Ligands: POV.34 Ligand excluded by PLIP POV.39: 2 residues within 4Å: Chain B: C.561, I.564 Ligand excluded by PLIP POV.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP POV.41: 18 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, L.359, K.369, S.370, W.373, L.374, W.395, L.396, L.400 Ligand excluded by PLIP POV.42: 7 residues within 4Å: Chain B: R.236, F.240, E.318, F.322, F.366, Y.367 Ligands: POV.29 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 5 residues within 4Å: Chain A: Y.558, C.561, E.565, F.609 Ligands: POV.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.558, A:F.609 CLR.32: 5 residues within 4Å: Chain B: Y.558, C.561, E.565, F.609 Ligands: POV.37 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.558, B:F.609

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, R. et al., Human XPR1 structures reveal phosphate export mechanism. Nature (2024)

Release Date

2024-07-03

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