SMTL ID : 6v4s.1

A Closed pore conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.55 Å

Oligo State

homo-pentamer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.479 Chain E: E.347, P.434, F.436 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Metal complexes: A:E.479, A:E.479, E:E.347, E:E.347, E:P.434 CA.2: 4 residues within 4Å: Chain A: E.347, P.434, F.436 Chain B: E.479 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.347, A:P.434, A:F.436, B:E.479, B:E.479 CA.8: 4 residues within 4Å: Chain B: E.347, P.434, F.436 Chain C: E.479 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Metal complexes: C:E.479, B:E.347, B:E.347, B:P.434, B:F.436 CA.16: 4 residues within 4Å: Chain C: E.347, P.434, F.436 Chain D: E.479 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:E.347, C:E.347, C:P.434, C:F.436, D:E.479 CA.22: 4 residues within 4Å: Chain D: E.347, P.434, F.436 Chain E: E.479 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Metal complexes: E:E.479, E:E.479, D:E.347, D:E.347, D:P.434

7 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: E.547 Chain B: E.547 Chain C: E.547 Chain D: E.547 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.547 NA.4: 2 residues within 4Å: Chain A: V.340, G.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.339 NA.5: 2 residues within 4Å: Chain A: R.345 Chain B: E.481 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.345 NA.13: 2 residues within 4Å: Chain B: R.345 Chain C: E.481 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.481 NA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.18: 1 residues within 4Å: Chain D: E.481 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.481 NA.23: 2 residues within 4Å: Chain D: R.345 Chain E: E.481 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.339, E:E.481

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain A: N.560 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: N.560 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: N.560 Chain D: F.559 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain D: N.560 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain E: N.560 Ligand excluded by PLIP

10 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.7: 5 residues within 4Å: Chain A: E.480, N.514, E.516 Chain E: L.439, F.635 No protein-ligand interaction detected (PLIP) LMT.10: 4 residues within 4Å: Chain A: R.634, F.635 Chain B: E.480, E.516 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.480 LMT.11: 4 residues within 4Å: Chain B: L.439, R.634, F.635 Chain C: E.516 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.634, C:E.516 LMT.12: 3 residues within 4Å: Chain A: R.599 Chain B: F.538, T.614 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.614 LMT.15: 5 residues within 4Å: Chain B: R.599, V.603 Chain C: K.540, T.614, L.617 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.540, B:R.599 LMT.20: 4 residues within 4Å: Chain C: L.439, R.634, F.635 Chain D: E.516 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.634, C:R.634 LMT.21: 2 residues within 4Å: Chain C: R.599 Chain D: T.614 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.599, C:R.599 LMT.25: 4 residues within 4Å: Chain D: L.439, R.634, F.635 Chain E: E.516 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.634, E:E.516 LMT.26: 4 residues within 4Å: Chain D: R.599, V.603 Chain E: K.540, T.614 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:K.540, D:R.599, D:R.599 LMT.27: 5 residues within 4Å: Chain A: F.538, K.540, T.614 Chain E: R.599, V.603 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:T.614 Hydrogen bonds: A:K.540, A:K.540, E:R.599, E:R.599

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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