SMTL ID : 8if3.1

Structure of human alpha-2/delta-1 with mirogabalin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.23 Å

Oligo State

monomer

Ligands

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

NAG-NAG.1: 8 residues within 4Å: Chain A: W.113, E.182, N.468, T.470, T.477, K.480, N.481, L.485 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: D.43, L.47, G.724, S.816, N.820 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: P.592, N.594 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.594 NAG.4: 4 residues within 4Å: Chain A: K.88, L.89, N.92, D.200 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.89 Hydrogen bonds: A:K.88, A:N.92, A:D.200 NAG.5: 3 residues within 4Å: Chain A: T.568, R.570, N.585 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.570 NAG.6: 3 residues within 4Å: Chain A: F.776, N.777, R.869 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.776 Hydrogen bonds: A:N.777 NAG.8: 5 residues within 4Å: Chain A: Q.112, D.116, F.117, N.120, N.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.112, A:D.116 NAG.9: 3 residues within 4Å: Chain A: L.572, F.890, N.891 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.891 NAG.10: 2 residues within 4Å: Chain A: N.663, T.665 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.663

1 x 8X9: 2-[(1R,5S,6S)-6-(aminomethyl)-3-ethyl-6-bicyclo[3.2.0]hept-3-enyl]acetic acid(Non-covalent)

8X9.7: 11 residues within 4Å: Chain A: W.205, V.207, A.215, Y.217, Y.236, R.241, W.243, Y.450, D.452, A.453, D.491 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.205, A:V.207, A:V.207, A:A.215, A:Y.217, A:Y.217, A:Y.236, A:W.243 Hydrogen bonds: A:Y.236, A:Y.450, A:D.452, A:D.452, A:A.453 Salt bridges: A:R.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozai, D. et al., Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human alpha 2 delta 1, a Voltage-Gated Calcium Channel Subunit. J.Mol.Biol. (2023)

Release Date

2023-04-05

Peptides

Voltage-dependent calcium channel subunit alpha-2/delta-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Voltage-dependent calcium channel subunit alpha-2/delta-1

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