SMTL ID : 6e1n.1

Structure of AtTPC1(DDE) in state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.2: 2 residues within 4Å: Chain A: F.358, D.366 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.366 CA.3: 4 residues within 4Å: Chain A: D.325, D.327, N.329, E.331 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.325, A:D.327, A:E.331 CA.13: 2 residues within 4Å: Chain A: M.619 Chain B: M.619 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: D.366 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.366, B:D.366 CA.15: 4 residues within 4Å: Chain B: D.325, D.327, N.329, E.331 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.325, B:D.327, B:E.331

16 x PLM: PALMITIC ACID(Non-covalent)(Covalent)

PLM.4: 6 residues within 4Å: Chain A: M.214, S.240, G.242, L.245 Ligands: PLM.5, PLM.8 Ligand excluded by PLIP PLM.5: 11 residues within 4Å: Chain A: M.214, S.240, G.242, A.243, L.245, Y.246, W.636, I.639, V.643 Ligands: PLM.4, PLM.10 Ligand excluded by PLIP PLM.6: 2 residues within 4Å: Chain A: I.183, V.576 Ligand excluded by PLIP PLM.7: 7 residues within 4Å: Chain A: I.568, Y.569, I.572, V.576, W.637, S.638, I.648 Ligand excluded by PLIP PLM.8: 4 residues within 4Å: Chain A: F.219, W.222, Y.241 Ligands: PLM.4 Ligand excluded by PLIP PLM.9: 12 residues within 4Å: Chain A: R.269, W.270, V.273, V.276 Chain B: E.101, L.102, F.563, L.566, V.611, F.614, L.617 Ligands: PLM.23 Ligand excluded by PLIP PLM.10: 7 residues within 4Å: Chain A: T.635, W.636, W.637, T.640, V.643, S.644 Ligands: PLM.5 Ligand excluded by PLIP PLM.11: 12 residues within 4Å: Chain A: L.559, I.562, L.566, P.607, M.610, V.611, F.614, L.617 Chain B: R.269, S.272, V.276 Ligands: PLM.21 Ligand excluded by PLIP PLM.16: 6 residues within 4Å: Chain B: M.214, S.240, G.242, L.245 Ligands: PLM.17, PLM.20 Ligand excluded by PLIP PLM.17: 11 residues within 4Å: Chain B: M.214, S.240, G.242, A.243, L.245, Y.246, W.636, I.639, V.643 Ligands: PLM.16, PLM.22 Ligand excluded by PLIP PLM.18: 4 residues within 4Å: Chain B: Y.179, I.183, V.576 Ligands: PLM.19 Ligand excluded by PLIP PLM.19: 8 residues within 4Å: Chain B: I.568, Y.569, I.572, V.576, W.637, Y.641, I.648 Ligands: PLM.18 Ligand excluded by PLIP PLM.20: 4 residues within 4Å: Chain B: F.219, W.222, Y.241 Ligands: PLM.16 Ligand excluded by PLIP PLM.21: 6 residues within 4Å: Chain A: E.101, L.102 Chain B: W.270, V.273 Ligands: PLM.11, 3PH.12 Ligand excluded by PLIP PLM.22: 7 residues within 4Å: Chain B: T.635, W.636, W.637, T.640, V.643, S.644 Ligands: PLM.17 Ligand excluded by PLIP PLM.23: 9 residues within 4Å: Chain A: L.280 Chain B: P.80, L.102, L.559, I.562, F.563, L.617 Ligands: PLM.9, 3PH.24 Ligand excluded by PLIP

2 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Covalent)

3PH.12: 11 residues within 4Å: Chain A: F.69, F.77, I.189, R.190, E.191, R.488, M.556, G.560, F.563 Chain B: L.280 Ligands: PLM.21 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.69, A:F.69, A:F.77, A:I.189, A:E.191, A:E.191, A:M.556, A:F.563, B:L.280 Hydrogen bonds: A:E.191 Salt bridges: A:R.488, A:R.488 3PH.24: 15 residues within 4Å: Chain A: L.280 Chain B: F.69, F.73, F.77, I.189, R.190, E.191, L.192, R.488, F.489, M.556, L.559, G.560, F.563 Ligands: PLM.23 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.69, B:F.69, B:F.77, B:I.189, B:E.191, B:E.191, B:L.192, B:M.556, B:F.563, B:F.563, A:L.280 Hydrogen bonds: B:R.190 Salt bridges: B:R.488, B:R.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kintzer, A.F. et al., Structural basis for activation of voltage sensor domains in an ion channel TPC1. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-19

Peptides

Two pore calcium channel protein 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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Two pore calcium channel protein 1

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