SMTL ID : 5j0z.1

Crystal structure of GLIC in complex with DHA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-pentamer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: F.74, R.81 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: R.73, F.74, R.81 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain E: R.73, F.74, R.81 Ligand excluded by PLIP

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-functional Binders)(Non-covalent)

LMT.2: 4 residues within 4Å: Ligands: LMT.3, LMT.4, LMT.10, LMT.18 No protein-ligand interaction detected (PLIP) LMT.3: 8 residues within 4Å: Chain A: I.232, A.233, I.236, L.237 Chain B: I.236 Chain E: A.233 Ligands: LMT.2, LMT.4 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: A:I.232, A:I.236, A:L.237, E:A.233, B:I.236 LMT.4: 5 residues within 4Å: Chain A: A.233 Chain B: I.232, A.233 Ligands: LMT.2, LMT.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.233, B:I.232 LMT.10: 6 residues within 4Å: Chain B: A.233 Chain C: I.232, A.233, I.236 Ligands: LMT.2, LMT.17 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.233, C:I.232, C:I.236 LMT.17: 4 residues within 4Å: Chain D: A.233, L.237 Chain E: I.236 Ligands: LMT.10 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.237, E:I.236 LMT.18: 6 residues within 4Å: Chain A: I.236 Chain D: A.233 Chain E: I.232, A.233, L.237 Ligands: LMT.2 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: E:I.232, E:L.237, A:I.236, D:A.233

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: K.34, N.79, R.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.79 Salt bridges: A:K.34 SO4.6: 4 residues within 4Å: Chain A: E.78, R.105 Chain E: S.25, K.34 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Salt bridges: A:R.105 Hydrogen bonds: E:S.25 SO4.11: 3 residues within 4Å: Chain A: S.25, K.34 Chain B: R.105 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.25 Salt bridges: A:K.34, B:R.105 SO4.12: 3 residues within 4Å: Chain B: S.25, K.34 Chain C: R.105 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.105, B:K.34 Hydrogen bonds: B:S.25 SO4.14: 4 residues within 4Å: Chain C: S.25, K.34 Chain D: E.78, R.105 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.25 Salt bridges: C:K.34, D:R.105 SO4.21: 2 residues within 4Å: Chain D: S.25 Chain E: R.105 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Salt bridges: E:R.105 Hydrogen bonds: D:S.25, D:S.25

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 7 residues within 4Å: Chain A: R.73, V.75, I.127, L.172, E.177 Chain E: F.38, R.101 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Salt bridges: E:R.101, A:R.73 Hydrophobic interactions: A:I.127 ACT.22: 5 residues within 4Å: Chain D: F.38, R.101 Chain E: R.73, I.127, E.177 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Salt bridges: D:R.101, E:R.73 Hydrophobic interactions: E:I.127

5 x HXA: DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID(Non-covalent)(Non-functional Binders)

HXA.8: 2 residues within 4Å: Chain A: R.113, R.114 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.114 HXA.13: 2 residues within 4Å: Chain B: R.113, R.114 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.114 HXA.15: 2 residues within 4Å: Chain C: R.114, M.248 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.114 HXA.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HXA.23: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.114

1 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.9: 9 residues within 4Å: Chain A: F.117, Y.190, I.194, I.198, L.199, L.202, Y.250, N.303, F.311 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.117, A:I.194, A:I.198, A:L.199, A:L.202, A:F.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basak, S. et al., Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel. Elife (2017)

Release Date

2017-03-15

Peptides

Proton-gated ion channel: 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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Proton-gated ion channel

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