SMTL ID : 6v4a.1

An open conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.83 Å

Oligo State

homo-pentamer

Ligands

5 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 9 residues within 4Å: Chain A: D.122, D.123, G.125, G.126, K.127, G.128, S.130, A.131, S.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.127, A:G.128, A:S.130, A:S.132, A:S.132 TRS.4: 8 residues within 4Å: Chain B: D.122, D.123, G.125, K.127, G.128, S.130, A.131, S.132 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.127, B:G.128, B:S.130, B:S.132, B:S.132 TRS.6: 8 residues within 4Å: Chain C: D.122, D.123, G.125, K.127, G.128, S.130, A.131, S.132 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:Q.277, C:K.127, C:G.128, C:S.130, C:S.132, C:S.132 TRS.7: 8 residues within 4Å: Chain D: D.122, D.123, G.125, K.127, G.128, S.130, A.131, S.132 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.122, D:K.127, D:G.128, D:S.130, D:S.132, D:S.132 TRS.9: 8 residues within 4Å: Chain D: Q.277 Chain E: D.122, D.123, K.127, G.128, S.130, A.131, S.132 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:Q.277, E:D.122, E:K.127, E:G.128, E:S.130, E:S.132, E:S.132

5 x P3A: PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL(Non-covalent)

P3A.2: 8 residues within 4Å: Chain A: Y.517, R.521 Chain E: Y.441, N.560, I.563, G.565, L.567, D.577 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.441, E:I.563, E:L.567 Hydrogen bonds: E:N.560, A:Y.517, A:Y.517 P3A.3: 7 residues within 4Å: Chain A: N.560, G.565, L.567, R.569, D.577 Chain B: Y.517, R.521 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.577 Hydrogen bonds: A:N.560, A:D.577 P3A.5: 7 residues within 4Å: Chain B: N.560, L.567, D.577, I.581 Chain C: Y.517, R.521, T.562 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.560, B:D.577 P3A.8: 4 residues within 4Å: Chain C: F.561, R.569 Chain D: Y.517, T.562 No protein-ligand interaction detected (PLIP) P3A.10: 5 residues within 4Å: Chain D: G.565, L.567, R.569 Chain E: Y.517, T.562 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:Y.517, E:T.562, D:G.565

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, H. et al., Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-06-03

Peptides

Neur_chan_LBD domain-containing protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
D

D
C

E
B

Membrane

We predict this structure to be a membrane protein.
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Neur_chan_LBD domain-containing protein

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