SMTL ID : 8on7.1

FMRFa-bound Malacoceros FaNaC1 in lipid nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x PHE- MET- ARG- PHE- NH2: FMRFamide, neuropeptide(Non-covalent)

PHE-MET-ARG-PHE-NH2.1: 13 residues within 4Å: Chain A: F.98, D.102, P.104, V.123, A.127, F.130, W.131, Q.134, E.236, R.238, M.239, P.241 Chain C: F.432 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.98, A:V.123, A:A.127, A:F.130, A:M.239, A:P.241 Hydrogen bonds: A:Q.134, A:Q.134, A:R.238, A:R.238, A:M.239, A:M.239 Salt bridges: A:D.102, A:E.236 PHE-MET-ARG-PHE-NH2.2: 13 residues within 4Å: Chain A: F.432 Chain B: F.98, D.102, P.104, V.123, A.127, F.130, W.131, Q.134, E.236, R.238, M.239, P.241 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.98, B:V.123, B:A.127, B:F.130, B:M.239, B:P.241 Hydrogen bonds: B:Q.134, B:Q.134, B:R.238, B:R.238, B:M.239, B:M.239 Salt bridges: B:D.102, B:E.236 PHE-MET-ARG-PHE-NH2.3: 13 residues within 4Å: Chain B: F.432 Chain C: F.98, D.102, P.104, V.123, A.127, F.130, W.131, Q.134, E.236, R.238, M.239, P.241 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.98, C:V.123, C:A.127, C:F.130, C:M.239, C:P.241 Hydrogen bonds: C:Q.134, C:Q.134, C:R.238, C:R.238, C:M.239, C:M.239 Salt bridges: C:D.102, C:E.236

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 2 residues within 4Å: Chain A: N.181, R.184 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: P.296, P.297, H.298, G.299, N.300, F.403 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.181, R.184 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: P.296, P.297, H.298, G.299, N.300, F.403 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.181, R.184 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain C: P.296, P.297, H.298, G.299, N.300, F.403 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: Y.327, N.393, A.396 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.393 NAG.11: 3 residues within 4Å: Chain A: E.442, N.445, Y.453 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.442 Hydrogen bonds: A:N.445, A:Y.453 NAG.12: 5 residues within 4Å: Chain A: K.458, Y.459, N.461, S.463, N.464 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.461, A:N.464 NAG.13: 3 residues within 4Å: Chain B: Y.327, N.393, A.396 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.393 NAG.14: 3 residues within 4Å: Chain B: E.442, N.445, Y.453 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.442 Hydrogen bonds: B:N.445, B:Y.453 NAG.15: 5 residues within 4Å: Chain B: K.458, Y.459, N.461, S.463, N.464 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.461, B:N.464 NAG.16: 3 residues within 4Å: Chain C: Y.327, N.393, A.396 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.393 NAG.17: 3 residues within 4Å: Chain C: E.442, N.445, Y.453 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.442 Hydrogen bonds: C:N.445, C:Y.453 NAG.18: 5 residues within 4Å: Chain C: K.458, Y.459, N.461, S.463, N.464 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.461, C:N.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalienkova, V. et al., Structural basis for excitatory neuropeptide signaling. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-02-14

Peptides

FMRFamide-gated sodium channel 1 (FaNaC1): 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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FMRFamide-gated sodium channel 1 (FaNaC1)

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