SMTL ID : 5egi.1

Structure of a Trimeric Intracellular Cation channel from C. elegans with bound Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-trimer

Ligands

3 x PT5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

PT5.1: 30 residues within 4Å: Chain A: M.38, E.41, M.68, L.79, K.129, R.133, L.157, A.161, A.164, G.165, S.166, G.167, I.168, R.170, H.184, N.185, E.186, P.190, S.191, T.194 Chain B: S.60, L.63, S.64, L.67, F.74, F.78, V.84, I.85, R.177 Ligands: PT5.2 20 PLIP interactions: 9 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.63, B:L.67, B:L.67, B:F.74, B:F.74, B:F.78, B:V.84, B:I.85, B:R.177, A:L.79, A:L.157 Hydrogen bonds: A:R.133, A:S.166, A:S.166, A:G.167, A:E.186, A:E.186 Salt bridges: A:K.129, A:R.133, A:R.170 PT5.2: 28 residues within 4Å: Chain B: M.38, E.41, F.78, L.79, K.129, R.133, A.164, G.165, S.166, G.167, I.168, R.170, H.184, E.186, A.193, T.194 Chain C: S.60, L.63, S.64, L.67, F.74, L.75, F.78, V.176, R.177 Ligands: PT5.1, PT5.4, DMU.5 24 PLIP interactions: 15 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:F.78, C:L.63, C:L.67, C:L.67, C:F.74, C:F.74, C:L.75, C:F.78, C:V.176, C:R.177 Hydrogen bonds: B:E.41, B:R.133, B:S.166, B:S.166, B:S.166, B:G.167, B:H.184, B:T.194, B:T.194 Salt bridges: B:K.129, B:R.133, B:R.170, B:H.184, B:H.184 PT5.4: 29 residues within 4Å: Chain A: L.67, F.74, L.75, F.78, V.84, F.88, L.172, E.173, V.176 Chain C: E.41, M.68, F.78, L.79, K.129, R.133, L.157, T.160, A.161, A.164, G.165, S.166, G.167, I.168, R.170, H.184, P.190, A.193, T.194 Ligands: PT5.2 23 PLIP interactions: 11 interactions with chain A, 12 interactions with chain C Hydrophobic interactions: A:L.67, A:L.67, A:F.74, A:F.74, A:F.74, A:L.75, A:F.78, A:V.84, A:F.88, A:L.172, A:V.176, C:F.78, C:L.79, C:L.157, C:I.168 Hydrogen bonds: C:R.133, C:R.133, C:A.164, C:S.166, C:S.166, C:G.167 Salt bridges: C:K.129, C:R.133

1 x CA: CALCIUM ION(Non-functional Binders)

CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.5: 11 residues within 4Å: Chain B: L.157, T.194, V.198 Chain C: F.53, H.57, L.59, S.60, W.62, L.63, R.177 Ligands: PT5.2 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.59, C:L.59, C:W.62, C:L.63, B:L.157, B:V.198, B:V.198 Hydrogen bonds: C:S.60, B:T.194 Salt bridges: C:H.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H.T. et al., Pore architecture of TRIC channels and insights into their gating mechanism. Nature (2016)

Release Date

2016-10-05

Peptides

Uncharacterized protein Y57A10A.10: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Uncharacterized protein Y57A10A.10