SMTL ID : 6x9h.1

Molecular mechanism and structural basis of small-molecule modulation of acid-sensing ion channel 1 (ASIC1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-trimer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: I.257, N.342 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.257 NAG.4: 1 residues within 4Å: Chain B: N.342 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain C: N.342 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.342

3 x UZG: 2-[4-(3,4-dimethoxyphenoxy)phenyl]-1H-benzimidazole-6-carboximidamide(Non-covalent)

UZG.2: 16 residues within 4Å: Chain A: E.73, L.90, L.91, A.92, M.130, Y.134, L.206, P.207, V.208, E.214, R.300, M.301, V.302, Y.310, C.311, Y.316 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.90, A:L.91, A:E.214, A:Y.316, A:Y.316 Hydrogen bonds: A:L.90, A:L.91, A:P.207, A:V.302 UZG.5: 16 residues within 4Å: Chain B: E.73, L.90, L.91, M.130, Y.134, L.206, P.207, V.208, E.214, R.300, M.301, V.302, H.303, Y.310, C.311, Y.316 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.90, B:L.91 Hydrogen bonds: B:L.90, B:L.91, B:P.207, B:V.302 pi-Stacking: B:Y.316 UZG.7: 17 residues within 4Å: Chain C: E.73, F.74, L.90, L.91, M.130, Y.134, L.206, P.207, V.208, E.214, T.215, R.300, M.301, V.302, Y.310, C.311, Y.316 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.90, C:L.91, C:M.130, C:L.206, C:E.214, C:E.214, C:Y.316 Hydrogen bonds: C:L.90, C:L.91, C:P.207, C:V.302

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

NA.3: 3 residues within 4Å: Chain A: D.408 Chain B: D.408 Chain C: D.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Molecular mechanism and structural basis of small-molecule modulation of the gating of acid-sensing ion channel 1. Commun Biol (2021)

Release Date

2020-12-30

Peptides

Acid-sensing ion channel 1: 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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Acid-sensing ion channel 1

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