SMTL ID : 6e1k.1

Structure of AtTPC1(DDE) reconstituted in saposin A with cat06 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

CA.1: 1 residues within 4Å: Ligands: CA.13 No protein-ligand interaction detected (PLIP) CA.2: 2 residues within 4Å: Chain A: D.596 Chain B: D.596 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: E.364, D.366 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.364 CA.4: 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: 3 residues within 4Å: Chain A: M.619 Chain B: M.619 Ligands: CA.1 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: E.364 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.364, B:E.364 CA.15: 4 residues within 4Å: Chain B: D.325, D.327, N.329, E.331 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.325, B:D.327, B:D.327, B:E.331

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

PLM.5: 7 residues within 4Å: Chain A: M.214, S.240, Y.241, G.242, L.245 Ligands: PLM.6, PLM.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.241, A:L.245 Hydrogen bonds: A:S.240, A:Y.241, A:G.242 PLM.6: 11 residues within 4Å: Chain A: W.213, L.217, G.242, A.243, Y.246, F.249, W.636, I.639, V.643 Ligands: PLM.5, PLM.11 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.213, A:W.213, A:L.217, A:Y.246, A:F.249, A:W.636, A:W.636, A:W.636, A:I.639, A:V.643, A:V.643 PLM.7: 5 residues within 4Å: Chain A: Y.179, I.183, I.568, V.576 Ligands: PLM.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.179, A:Y.179, A:I.183, A:I.568, A:V.576 PLM.8: 8 residues within 4Å: Chain A: I.568, Y.569, I.572, V.576, T.633, W.637, S.638 Ligands: PLM.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.569, A:Y.569, A:I.572, A:I.572, A:V.576 Hydrogen bonds: A:S.638 PLM.9: 5 residues within 4Å: Chain A: L.218, F.219, W.222, Y.241 Ligands: PLM.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.219, A:W.222, A:W.222, A:W.222, A:Y.241, A:Y.241 PLM.10: 9 residues within 4Å: Chain A: R.269, W.270, V.276 Chain B: E.101, L.566, M.610, V.611, F.614, L.617 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.101, B:L.566, B:V.611, B:F.614, B:F.614, B:L.617, A:R.269, A:W.270, A:V.276 PLM.11: 5 residues within 4Å: Chain A: W.636, W.637, T.640, V.643 Ligands: PLM.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.637 Hydrogen bonds: A:W.636 PLM.12: 10 residues within 4Å: Chain A: E.101, L.102, L.566, M.610, V.611, F.614, L.617 Chain B: R.269, W.270, V.276 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.101, A:L.102, A:L.566, A:V.611, A:F.614, A:F.614, A:L.617, B:R.269, B:W.270, B:V.276 Hydrogen bonds: A:E.101 PLM.16: 8 residues within 4Å: Chain B: M.214, S.240, Y.241, G.242, L.245 Ligands: PLM.17, PLM.20, PLM.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.241, B:L.245 PLM.17: 11 residues within 4Å: Chain B: W.213, M.214, S.240, G.242, A.243, L.245, F.249, W.636, V.643 Ligands: PLM.16, PLM.21 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.213, B:L.245, B:F.249, B:W.636, B:W.636, B:W.636 PLM.18: 5 residues within 4Å: Chain B: Y.179, I.183, I.568, V.576 Ligands: PLM.19 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.179, B:Y.179, B:I.183, B:I.568, B:V.576 PLM.19: 10 residues within 4Å: Chain B: I.568, Y.569, I.572, V.576, T.633, T.635, W.637, S.638, S.644 Ligands: PLM.18 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.569, B:Y.569, B:I.572, B:I.572, B:V.576 Hydrogen bonds: B:S.638 PLM.20: 6 residues within 4Å: Chain B: L.218, F.219, W.222, F.225, Y.241 Ligands: PLM.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.219, B:W.222, B:W.222, B:F.225, B:Y.241 PLM.21: 8 residues within 4Å: Chain B: T.635, W.636, W.637, T.640, V.643, V.647 Ligands: PLM.16, PLM.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.636, B:V.643, B:V.647 Hydrogen bonds: B:T.635

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
cat06 light chain: CE
cat06 heavy chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
E

D
D

F
F

Membrane

We predict this structure to be a membrane protein.
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Two pore calcium channel protein 1

cat06 light chain

cat06 heavy chain

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