SMTL ID : 6fgc.1

Crystal structure of Gephyrin E domain in complex with Artesunate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-functional Binders)

CA.1: 2 residues within 4Å: Chain A: G.256 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) CA.18: 2 residues within 4Å: Chain B: G.256 Ligands: ADP.19 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 25 residues within 4Å: Chain A: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, G.260, D.263, G.309, N.310, P.311 Chain B: D.57, T.96, G.97, R.141 Ligands: CA.1 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.188, A:D.207, A:D.207, A:S.208, A:N.209, A:G.256, A:V.257, A:S.258, A:D.263, A:G.309, B:D.57, B:R.141 Water bridges: A:E.192, A:E.192, A:N.209, A:N.209, A:S.258, A:N.310, B:T.96, B:G.97, B:G.97 ADP.19: 25 residues within 4Å: Chain A: D.57, T.96, G.97, R.141 Chain B: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, G.260, D.263, G.309, N.310, P.311 Ligands: CA.18 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.188, B:E.192, B:D.207, B:S.208, B:N.209, B:G.256, B:V.257, B:S.258, B:D.263, B:G.309, A:D.57, A:R.141 Water bridges: B:E.192, B:E.192, B:N.209, B:N.209, B:S.258, B:N.310, A:T.96, A:G.97, A:G.97

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: V.183, S.246, R.247, A.248, D.249, K.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.249 Water bridges: A:K.302, A:K.302 Salt bridges: A:K.302 PO4.20: 6 residues within 4Å: Chain B: V.183, S.246, R.247, A.248, D.249, K.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.249 Water bridges: B:K.302, B:K.302 Salt bridges: B:K.302

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 11 residues within 4Å: Chain A: S.208, T.212, P.311, V.312, V.315, R.358 Chain B: S.163, G.166, L.167, T.170 Ligands: ACT.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.212, A:P.311, A:V.312 Hydrogen bonds: A:R.358, A:R.358 Water bridges: B:T.170 MPD.21: 11 residues within 4Å: Chain A: S.163, G.166, L.167, T.170 Chain B: S.208, T.212, P.311, V.312, V.315, R.358 Ligands: ACT.23 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.212, B:P.311, B:V.312 Hydrogen bonds: B:R.358, B:R.358 Water bridges: A:T.170

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 6 residues within 4Å: Chain A: L.227, G.228, I.229, V.230, A.240, E.243 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.227, A:A.240 Hydrogen bonds: A:E.243 MRD.22: 6 residues within 4Å: Chain B: L.227, G.228, I.229, V.230, A.240, E.243 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.227, B:A.240 Hydrogen bonds: B:E.243

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

ACT.6: 7 residues within 4Å: Chain A: N.310, P.311, V.312 Chain B: L.48, R.141, D.146 Ligands: MPD.4 Ligand excluded by PLIP ACT.7: 3 residues within 4Å: Chain A: N.195, E.197 Chain B: R.31 Ligand excluded by PLIP ACT.8: 6 residues within 4Å: Chain A: E.18, M.19, T.20, P.21, V.22, R.301 Ligand excluded by PLIP ACT.9: 1 residues within 4Å: Chain A: E.18 Ligand excluded by PLIP ACT.10: 4 residues within 4Å: Chain A: L.6, T.7, S.8, F.283 Ligand excluded by PLIP ACT.11: 4 residues within 4Å: Chain A: L.6, F.283, L.288, R.353 Ligand excluded by PLIP ACT.12: 5 residues within 4Å: Chain A: D.334, R.336, P.337, T.338 Chain B: R.387 Ligand excluded by PLIP ACT.13: 4 residues within 4Å: Chain A: T.25, A.39, K.156, N.179 Ligand excluded by PLIP ACT.14: 1 residues within 4Å: Chain A: V.22 Ligand excluded by PLIP ACT.15: 5 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 Chain B: S.385 Ligand excluded by PLIP ACT.23: 7 residues within 4Å: Chain A: L.48, R.141, D.146 Chain B: N.310, P.311, V.312 Ligands: MPD.21 Ligand excluded by PLIP ACT.24: 3 residues within 4Å: Chain A: R.31 Chain B: N.195, E.197 Ligand excluded by PLIP ACT.25: 6 residues within 4Å: Chain B: E.18, M.19, T.20, P.21, V.22, R.301 Ligand excluded by PLIP ACT.26: 1 residues within 4Å: Chain B: E.18 Ligand excluded by PLIP ACT.27: 4 residues within 4Å: Chain B: L.6, T.7, S.8, F.283 Ligand excluded by PLIP ACT.28: 4 residues within 4Å: Chain B: L.6, F.283, L.288, R.353 Ligand excluded by PLIP ACT.29: 5 residues within 4Å: Chain A: R.387 Chain B: D.334, R.336, P.337, T.338 Ligand excluded by PLIP ACT.30: 4 residues within 4Å: Chain B: T.25, A.39, K.156, N.179 Ligand excluded by PLIP ACT.31: 1 residues within 4Å: Chain B: V.22 Ligand excluded by PLIP ACT.32: 5 residues within 4Å: Chain A: S.385 Chain B: C.152, V.153, L.154, A.155 Ligand excluded by PLIP

2 x D95: Artesunate(Non-covalent)

D95.16: 12 residues within 4Å: Chain A: M.9, D.10, F.13, I.14, L.17, L.320, R.336, P.337, I.339, Y.356, M.394, M.414 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.10, A:F.13, A:F.13, A:R.336, A:I.339 Hydrogen bonds: A:R.336 Salt bridges: A:R.336, A:R.336, A:R.336, A:R.336 D95.33: 12 residues within 4Å: Chain B: M.9, D.10, F.13, I.14, L.17, L.320, R.336, P.337, I.339, Y.356, M.394, M.414 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.10, B:F.13, B:F.13, B:R.336, B:I.339 Hydrogen bonds: B:R.336 Salt bridges: B:R.336, B:R.336, B:R.336, B:R.336

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

CL.17: 7 residues within 4Å: Chain A: P.286, G.287, L.288, P.289, P.308, N.310, S.313 Ligand excluded by PLIP CL.34: 7 residues within 4Å: Chain B: P.286, G.287, L.288, P.289, P.308, N.310, S.313 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., Elucidating the Molecular Basis for Inhibitory Neurotransmission Regulation by Artemisinins. Neuron (2019)

Release Date

2019-01-16

Peptides

Gephyrin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Gephyrin

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