SMTL ID : 9jxi.1

Cryo-EM structure of human XPR1 with InsP8 in an 'arch-like' intermediate state of the SPX domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x I8P: (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)](Non-covalent)

I8P.1: 10 residues within 4Å: Chain A: K.1, F.2, Y.21, K.157, K.160, K.161, K.164 Chain B: R.156, K.160 Ligands: I8P.3 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.1, A:K.1, A:F.2, A:Y.21 Salt bridges: A:K.1, A:K.25, A:K.157, A:K.161, A:K.161, A:K.164, A:K.164, A:K.164, B:R.156, B:K.160 I8P.2: 4 residues within 4Å: Chain A: K.128, K.212, N.305, K.368 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.305 Salt bridges: A:K.128, A:K.128, A:K.212, A:K.212, A:K.212, A:K.212, A:K.363, A:K.363, A:K.363, A:K.368 I8P.3: 9 residues within 4Å: Chain A: R.156, K.160 Chain B: K.1, F.2, K.157, K.160, K.161, K.164 Ligands: I8P.1 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.1, B:K.1, B:K.1, B:F.2, B:Y.21 Salt bridges: B:K.1, B:K.25, B:K.157, B:K.161, B:K.161, B:K.164, B:K.164, B:K.164, A:R.156, A:K.160 I8P.4: 4 residues within 4Å: Chain B: K.128, K.212, N.305, K.368 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.305 Salt bridges: B:K.128, B:K.128, B:K.212, B:K.212, B:K.212, B:K.212, B:K.363, B:K.363, B:K.363, B:K.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Cryo-EM structure of human XPR1 in apo state. Mol.Cell (2025)

Release Date

2025-08-27

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.
Show / Hide

Solute carrier family 53 member 1