SMTL ID : 7l6q.1

Unliganded ELIC in styrene-maleic-acid nanodiscs at 2.5-Angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.1: 9 residues within 4Å: Chain A: A.217, W.224, Q.298, R.301, L.302, P.305 Chain B: L.278, H.285, Q.287 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.224, A:W.224, A:L.302, A:P.305, B:H.285 Hydrogen bonds: A:Q.298, A:R.301, A:R.301, B:H.285 Salt bridges: A:R.301 PGW.3: 9 residues within 4Å: Chain A: L.278, H.285, Q.287 Chain E: A.217, W.224, Q.298, R.301, L.302, P.305 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain E Hydrophobic interactions: A:H.285, E:W.224, E:W.224, E:L.302, E:P.305 Hydrogen bonds: A:H.285, A:Q.287, E:Q.298, E:R.301, E:R.301 Salt bridges: E:R.301 PGW.4: 9 residues within 4Å: Chain B: A.217, W.224, Q.298, R.301, L.302, P.305 Chain C: L.278, H.285, Q.287 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.224, B:W.224, B:L.302, B:P.305, C:H.285 Hydrogen bonds: B:Q.298, B:R.301, B:R.301, C:H.285 Salt bridges: B:R.301 PGW.6: 9 residues within 4Å: Chain C: A.217, W.224, Q.298, R.301, L.302, P.305 Chain D: L.278, H.285, Q.287 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.224, C:W.224, C:L.302, C:P.305, D:H.285 Hydrogen bonds: C:Q.298, C:R.301, C:R.301, D:H.285, D:Q.287 Salt bridges: C:R.301 PGW.8: 9 residues within 4Å: Chain D: A.217, W.224, Q.298, R.301, L.302, P.305 Chain E: L.278, H.285, Q.287 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:W.224, D:W.224, D:L.302, D:P.305, E:H.285 Hydrogen bonds: D:Q.298, D:R.301, D:R.301, E:H.285 Salt bridges: D:R.301

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 20 residues within 4Å: Chain A: T.259, Q.264, I.267, A.268, G.271, F.274, A.275, L.278, L.279, F.282, L.296, R.299, A.303, F.304, I.311, L.315 Chain E: L.205, W.206, L.210, G.213 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain A Hydrophobic interactions: E:L.205, E:L.205, E:W.206, E:L.210, A:F.274, A:L.279, A:F.282, A:F.282, A:L.296, A:R.299, A:A.303, A:F.304 Hydrogen bonds: A:Q.264 CDL.5: 20 residues within 4Å: Chain A: L.205, W.206, L.210, G.213 Chain B: T.259, Q.264, I.267, A.268, G.271, F.274, A.275, L.278, L.279, F.282, L.296, R.299, A.303, F.304, I.311, L.315 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.274, B:L.279, B:F.282, B:F.282, B:L.296, B:R.299, B:A.303, B:F.304, A:L.205, A:L.205, A:W.206, A:L.210 Hydrogen bonds: B:Q.264 CDL.7: 20 residues within 4Å: Chain B: L.205, W.206, L.210, G.213 Chain C: T.259, Q.264, I.267, A.268, G.271, F.274, A.275, L.278, L.279, F.282, L.296, R.299, A.303, F.304, I.311, L.315 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.274, C:L.279, C:F.282, C:F.282, C:L.296, C:R.299, C:A.303, C:F.304, B:L.205, B:L.205, B:W.206, B:L.210 Hydrogen bonds: C:Q.264 CDL.9: 20 residues within 4Å: Chain C: L.205, W.206, L.210, G.213 Chain D: T.259, Q.264, I.267, A.268, G.271, F.274, A.275, L.278, L.279, F.282, L.296, R.299, A.303, F.304, I.311, L.315 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.274, D:L.279, D:F.282, D:F.282, D:L.296, D:R.299, D:A.303, D:F.304, C:L.205, C:L.205, C:W.206, C:L.210 Hydrogen bonds: D:Q.264 CDL.10: 20 residues within 4Å: Chain D: L.205, W.206, L.210, G.213 Chain E: T.259, Q.264, I.267, A.268, G.271, F.274, A.275, L.278, L.279, F.282, L.296, R.299, A.303, F.304, I.311, L.315 13 PLIP interactions: 4 interactions with chain D, 9 interactions with chain E Hydrophobic interactions: D:L.205, D:L.205, D:W.206, D:L.210, E:F.274, E:L.279, E:F.282, E:F.282, E:L.296, E:R.299, E:A.303, E:F.304 Hydrogen bonds: E:Q.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-06-23

Peptides

Gamma-aminobutyric-acid receptor subunit beta-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric-acid receptor subunit beta-1

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