SMTL ID : 8ouo.1

Human TPC2 in Complex with Antagonist (S)-SG-094

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x PLD: di-heneicosanoyl phosphatidyl choline(Non-covalent)

PLD.1: 11 residues within 4Å: Chain A: N.155, L.156, W.157, F.193, L.196, L.206, K.207, R.210, I.585, V.589, I.684 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.196, A:L.206, A:L.206, A:I.585, A:V.589, A:I.684 Salt bridges: A:K.207 PLD.9: 12 residues within 4Å: Chain B: L.156, W.157, L.196, L.206, K.207, I.209, R.210, L.213, I.585, V.589, V.683, I.684 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.157, B:L.196, B:L.206, B:L.206, B:I.209, B:I.209, B:R.210, B:L.213, B:L.213, B:I.585, B:V.589, B:V.683, B:I.684 Salt bridges: B:K.207, B:K.207

3 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.2: 12 residues within 4Å: Chain A: F.553, L.556, I.559, P.560, A.566, A.569, S.570, L.573 Chain B: H.226, L.229, I.298 Ligands: Y01.13 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.553, A:L.556, A:I.559, A:A.569, A:L.573, B:L.229, B:I.298 Hydrogen bonds: A:S.570 Q7G.8: 7 residues within 4Å: Chain A: C.450, V.451, V.454, L.455 Chain B: M.232, L.258 Ligands: Q7G.14 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.451, A:V.454, A:L.455, B:L.258 Q7G.14: 5 residues within 4Å: Chain B: C.228, L.262, W.669 Ligands: Q7G.8, Y01.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.669

1 x W4E: (1S)-6-methoxy-2-methyl-7-phenoxy-1-[(4-phenoxyphenyl)methyl]-3,4-dihydro-1H-isoquinoline(Non-covalent)

W4E.3: 7 residues within 4Å: Chain A: D.435, Y.436, N.439, F.555, I.558, S.561 Chain B: I.225 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.436, A:N.439, A:F.555, A:F.555, A:I.558, B:I.225

2 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.4: 13 residues within 4Å: Chain A: Q.83, S.87, F.91, L.94, L.195, N.198, S.199, S.200, M.202, R.580, G.583, V.587, Y.590 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.91, A:L.94, A:L.195, A:V.587, A:V.587, A:Y.590, A:Y.590 Hydrogen bonds: A:S.199, A:S.200 Salt bridges: A:R.580 PCF.10: 15 residues within 4Å: Chain B: S.87, I.90, F.91, L.94, L.195, N.198, S.199, S.200, M.201, M.202, R.580, G.583, G.584, V.587, L.643 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.90, B:F.91, B:L.94, B:L.94, B:L.643 Hydrogen bonds: B:N.198, B:S.199, B:S.199, B:S.200, B:M.201, B:R.580

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 10 residues within 4Å: Chain A: G.220, L.223, L.227, P.259, T.263, L.266, P.668, W.669, I.672, V.675 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.223, A:L.227, A:P.259, A:L.266, A:W.669, A:W.669, A:W.669, A:I.672, A:V.675 Y01.6: 10 residues within 4Å: Chain A: L.229, F.230, F.233, K.284, N.285, Y.288, F.291, V.294 Chain B: V.552, F.553 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:V.552, B:F.553, A:L.229, A:F.230, A:F.230, A:F.230, A:F.233, A:F.233, A:F.233, A:Y.288, A:F.291, A:V.294 Salt bridges: A:K.284 Y01.7: 11 residues within 4Å: Chain A: F.98, S.104, L.105, T.106, A.640, V.644 Chain B: N.285, R.286, A.287, A.289, I.293 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.98, A:L.105, A:A.640, A:V.644, B:A.287, B:A.289, B:I.293 Y01.11: 11 residues within 4Å: Chain A: N.285, R.286, A.287, I.293 Chain B: F.98, S.104, L.105, T.106, S.107, A.640, V.644 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.98, B:L.105, B:A.640, B:V.644, A:A.287, A:I.293 Hydrogen bonds: B:S.107, B:S.107 Y01.12: 10 residues within 4Å: Chain B: G.220, L.223, P.259, T.263, L.266, P.668, W.669, K.671, V.675 Ligands: Q7G.14 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.223, B:L.266, B:W.669, B:W.669, B:K.671, B:V.675 Y01.13: 9 residues within 4Å: Chain B: L.229, F.230, F.233, N.285, A.287, Y.288, F.291, V.294 Ligands: Q7G.2 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.229, B:F.230, B:F.233, B:F.233, B:F.233, B:Y.288, B:Y.288, B:F.291, B:F.291, B:V.294 Hydrogen bonds: B:N.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, G. et al., Structural basis for inhibition of the lysosomal two-pore channel TPC2 by a small molecule antagonist. Structure (2024)

Release Date

2024-06-12

Peptides

Two pore channel protein 2: 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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Two pore channel protein 2