SMTL ID : 9g6c.1

CLC7/OSTM1 complex with bound PIP2 lipid

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: Y.94, E.95, S.96, S.632, P.634, V.635, T.636, N.657, H.658, N.659, G.660, F.661, R.767, H.768, L.781, T.783, R.784, K.785, D.786 Ligands: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:E.95, A:S.96, A:S.96, A:S.632, A:T.636, A:T.636, A:T.636, A:N.659, A:N.659, A:G.660, A:T.783, A:T.783 Water bridges: A:E.95, A:N.657, A:H.658, A:T.783, A:R.784, A:R.784, A:K.785, A:K.785 Salt bridges: A:H.658, A:R.767, A:R.767, A:H.768, A:K.785, A:K.785, A:K.785 pi-Stacking: A:H.658, A:H.658 ATP.11: 20 residues within 4Å: Chain C: Y.94, E.95, S.96, S.632, P.634, V.635, T.636, N.657, H.658, N.659, G.660, F.661, R.767, H.768, L.781, T.783, R.784, K.785, D.786 Ligands: MG.12 32 PLIP interactions: 32 interactions with chain C Hydrogen bonds: C:E.95, C:S.96, C:S.96, C:S.632, C:T.636, C:T.636, C:T.636, C:N.659, C:N.659, C:G.660, C:T.783, C:T.783 Water bridges: C:E.95, C:N.657, C:N.657, C:H.658, C:R.784, C:K.785, C:K.785, C:K.785, C:K.785, C:K.785, C:K.785 Salt bridges: C:H.658, C:R.767, C:R.767, C:H.768, C:K.785, C:K.785, C:K.785 pi-Stacking: C:H.658, C:H.658

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.95, N.659, K.785 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.95, H2O.4, H2O.4 MG.12: 4 residues within 4Å: Chain C: E.95, N.659, K.785 Ligands: ATP.11 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.95, H2O.11, H2O.12

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: G.245, E.247, G.248, G.512, V.513, F.514, I.515 Ligand excluded by PLIP CL.4: 7 residues within 4Å: Chain A: S.204, I.206, G.248, G.512, V.513, F.514, Y.602 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: A.202, G.203, S.204, G.205, P.207, Q.208 Ligand excluded by PLIP CL.13: 7 residues within 4Å: Chain C: G.245, E.247, G.248, G.512, V.513, F.514, I.515 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain C: S.204, I.206, G.248, G.512, V.513, F.514, Y.602 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain C: A.202, G.203, S.204, G.205, P.207, Q.208 Ligand excluded by PLIP

2 x 01: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1S,2R,3S,4R,5R,6R)-2,4,5-tris(oxidanyl)-3,6-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

01.6: 23 residues within 4Å: Chain A: L.132, L.136, V.140, V.222, R.223, L.224, L.227, V.256, A.259, G.260, I.261, Q.263, G.264, R.265, S.266, T.267, S.268, F.273, I.275, F.276, K.285, P.716, R.717 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.132, A:L.136, A:L.136, A:V.140, A:L.227, A:F.273, A:F.273, A:I.275, A:F.276 Hydrogen bonds: A:R.223, A:L.224, A:S.266, A:T.267, A:T.267, A:T.267, A:S.268, A:K.285, A:K.285, A:R.717 Water bridges: A:H.220, A:H.220, A:R.223, A:K.225, A:R.265, A:R.265, A:R.717 Salt bridges: A:R.223, A:R.265, A:R.717 01.16: 23 residues within 4Å: Chain C: L.132, L.136, V.222, R.223, L.224, L.227, V.256, I.257, A.259, G.260, I.261, Q.263, G.264, R.265, S.266, T.267, S.268, F.273, I.275, F.276, K.285, P.716, R.717 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:L.132, C:L.136, C:L.227, C:F.273, C:F.276 Hydrogen bonds: C:R.223, C:L.224, C:I.261, C:S.266, C:T.267, C:T.267, C:S.268, C:K.285, C:K.285, C:R.717 Water bridges: C:H.220, C:H.220, C:R.223, C:K.225, C:R.265, C:R.265, C:R.717 Salt bridges: C:R.223, C:R.265, C:R.717

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 8 residues within 4Å: Chain A: V.387, A.390, V.391, A.394, Y.397, F.597, I.598, E.599 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.387, A:V.387, A:A.390, A:V.391, A:A.394, A:Y.397, A:F.597, A:F.597, A:F.597, A:F.597, A:I.598 Y01.8: 10 residues within 4Å: Chain A: V.430, Y.433, S.434, F.453 Chain B: T.282, I.286, S.289, V.290, L.293, F.294 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.286, B:I.286, B:V.290, B:L.293, B:F.294, A:V.430, A:Y.433 Hydrogen bonds: B:T.282 Y01.9: 8 residues within 4Å: Chain A: V.189, I.193, I.197, K.225, V.228, I.229, S.232, L.236 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.189, A:I.193, A:I.197, A:V.228, A:L.236 Salt bridges: A:K.225 Y01.10: 8 residues within 4Å: Chain A: W.398, F.402, V.423, F.499, L.500, W.503 Chain B: Y.300, F.304 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.300, B:Y.300, A:V.423, A:F.499, A:L.500, A:W.503, A:W.503, A:W.503 Y01.17: 7 residues within 4Å: Chain C: V.387, A.390, V.391, A.394, Y.397, F.597, E.599 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.387, C:V.387, C:A.390, C:V.391, C:A.394, C:Y.397, C:F.597, C:F.597, C:F.597 Y01.18: 8 residues within 4Å: Chain C: V.430, Y.433, S.434, F.453 Chain D: I.286, S.289, L.293, F.294 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.430, D:I.286, D:I.286, D:L.293 Y01.19: 8 residues within 4Å: Chain C: F.143, V.147, L.151, I.193, I.197, K.225, S.232, I.235 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.143, C:V.147, C:L.151, C:I.193, C:I.197, C:I.235 Salt bridges: C:K.225 Y01.20: 6 residues within 4Å: Chain C: V.423, F.499, W.503 Chain D: Y.300, L.301, F.304 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.423, C:F.499, C:W.503, C:W.503, C:W.503, D:Y.300, D:Y.300, D:L.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilton, J. et al., Mechanism of phosphoinositide regulation of lysosomal pH via inhibition of CLC7. To Be Published

Release Date

2025-07-30

Peptides

H(+)/Cl(-) exchange transporter 7: AC
Osteopetrosis-associated transmembrane protein 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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H(+)/Cl(-) exchange transporter 7

Osteopetrosis-associated transmembrane protein 1

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