SMTL ID : 8x5b.1

Cryo-EM structures of human XPR1 in closed states

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: D.170, N.173, K.254, Y.255, R.342, W.345, R.376 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.170, A:D.170 Water bridges: A:K.254, A:R.342, A:R.375 Salt bridges: A:K.254, A:R.342, A:R.376 PO4.2: 5 residues within 4Å: Chain A: W.300, M.304, D.305, R.383, C.392 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.304, A:M.304 Water bridges: A:R.383 Salt bridges: A:R.383 PO4.3: 7 residues within 4Å: Chain A: R.42, R.45, M.180, D.181, Y.184, H.213, R.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.181, A:D.181, A:D.181 Salt bridges: A:R.45, A:R.220 PO4.4: 6 residues within 4Å: Chain A: V.161, F.166, R.231, R.238, N.251, F.395 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.251 Salt bridges: A:R.231, A:R.238 PO4.14: 8 residues within 4Å: Chain B: D.170, N.173, K.254, Y.255, R.342, W.345, R.375, R.376 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.170, B:D.170, B:R.375 Water bridges: B:R.342, B:R.376 Salt bridges: B:K.254, B:R.342, B:R.376 PO4.15: 5 residues within 4Å: Chain B: W.300, M.304, D.305, R.383, C.392 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.392 Water bridges: B:R.383, B:R.383 Salt bridges: B:R.383 PO4.16: 7 residues within 4Å: Chain B: V.161, F.166, R.231, R.238, H.248, N.251, F.395 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.248, B:N.251 Salt bridges: B:R.231, B:R.238 PO4.17: 7 residues within 4Å: Chain B: R.42, R.45, M.180, D.181, Y.184, H.213, R.220 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.181, B:D.181 Salt bridges: B:R.42, B:R.45, B:R.220

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

POV.5: 16 residues within 4Å: Chain A: L.50, L.57, W.64, F.75, L.77, N.78, N.82, L.83, Y.124, M.127, K.141, S.142, W.145, W.167, I.178, L.182 Ligand excluded by PLIP POV.6: 9 residues within 4Å: Chain A: R.8, F.12, E.90, I.91, F.94, F.130, F.138, Y.139 Ligands: POV.7 Ligand excluded by PLIP POV.7: 3 residues within 4Å: Chain A: W.4, R.8 Ligands: POV.6 Ligand excluded by PLIP POV.8: 3 residues within 4Å: Chain A: S.102, A.105, P.110 Ligand excluded by PLIP POV.9: 1 residues within 4Å: Ligands: POV.18 Ligand excluded by PLIP POV.11: 5 residues within 4Å: Chain A: A.221, I.222, C.225, I.226, A.266 Ligand excluded by PLIP POV.12: 3 residues within 4Å: Chain A: F.48, I.363, T.366 Ligand excluded by PLIP POV.13: 4 residues within 4Å: Chain A: T.22, F.108 Ligands: POV.19, POV.24 Ligand excluded by PLIP POV.18: 13 residues within 4Å: Chain A: C.13, F.16, F.48, I.51, F.55, H.85, Q.86, F.89, A.92 Chain B: A.3, W.4 Ligands: POV.9, POV.23 Ligand excluded by PLIP POV.19: 3 residues within 4Å: Chain B: T.22, F.108 Ligands: POV.13 Ligand excluded by PLIP POV.20: 10 residues within 4Å: Chain A: A.3, F.7 Chain B: C.13, F.48, I.51, F.55, H.85, Q.86, A.92 Ligands: POV.25 Ligand excluded by PLIP POV.21: 16 residues within 4Å: Chain B: L.50, L.54, L.57, F.75, L.77, N.78, S.81, N.82, L.83, M.127, F.130, K.141, S.142, W.145, L.146, W.167 Ligand excluded by PLIP POV.22: 8 residues within 4Å: Chain B: R.8, F.12, E.90, I.91, F.94, F.138, Y.139 Ligands: POV.23 Ligand excluded by PLIP POV.23: 4 residues within 4Å: Chain B: W.4, R.8 Ligands: POV.18, POV.22 Ligand excluded by PLIP POV.24: 6 residues within 4Å: Chain B: S.102, A.105, F.108, P.110, Y.119 Ligands: POV.13 Ligand excluded by PLIP POV.25: 2 residues within 4Å: Ligands: POV.20, CLR.26 Ligand excluded by PLIP POV.27: 4 residues within 4Å: Chain B: I.222, C.225, W.229, T.263 Ligand excluded by PLIP POV.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.10: 4 residues within 4Å: Chain A: Y.325, C.333, E.337, F.381 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.325, A:F.381 CLR.26: 4 residues within 4Å: Chain B: C.333, E.337, F.381 Ligands: POV.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.337, B:F.381

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
F

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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