SMTL ID : 6fgd.1

Crystal structure of Gephyrin E domain in complex with Artemether

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: G.256 Ligands: ADP.29 No protein-ligand interaction detected (PLIP) CA.2: 4 residues within 4Å: Chain A: S.258, D.263 Chain B: T.96 Ligands: ADP.29 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.263, A:D.263, H2O.5, H2O.10, H2O.18 CA.32: 2 residues within 4Å: Chain B: G.256 Ligands: ADP.60 No protein-ligand interaction detected (PLIP) CA.33: 4 residues within 4Å: Chain A: T.96 Chain B: S.258, D.263 Ligands: ADP.60 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.263, B:D.263, H2O.2, H2O.22, H2O.26

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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.247, A:R.247, A:D.249 Water bridges: A:K.302, A:K.302 Salt bridges: A:K.302 PO4.34: 6 residues within 4Å: Chain B: V.183, S.246, R.247, A.248, D.249, K.302 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.247, B:R.247, B:D.249 Water bridges: B:K.302, B:K.302 Salt bridges: B:K.302

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

ACT.4: 5 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 Chain B: S.385 Ligand excluded by PLIP ACT.5: 7 residues within 4Å: Chain A: R.327, D.334, R.336, P.337, T.338 Chain B: R.387 Ligands: ACT.26 Ligand excluded by PLIP ACT.6: 8 residues within 4Å: Chain A: M.34, G.35, H.159, M.160, G.161 Chain B: S.388, R.418 Ligands: ACT.26 Ligand excluded by PLIP ACT.7: 7 residues within 4Å: Chain A: P.21, V.22, L.23, G.24, V.300, R.301 Ligands: ACT.18 Ligand excluded by PLIP ACT.8: 6 residues within 4Å: Chain A: P.311, V.312 Chain B: L.48, R.141, D.146 Ligands: MPD.30 Ligand excluded by PLIP ACT.9: 3 residues within 4Å: Chain A: L.6, S.8, F.283 Ligand excluded by PLIP ACT.10: 4 residues within 4Å: Chain A: L.6, F.283, L.288, R.353 Ligand excluded by PLIP ACT.11: 3 residues within 4Å: Chain A: Q.218 Chain B: R.31, D.32 Ligand excluded by PLIP ACT.12: 6 residues within 4Å: Chain A: E.26, R.36, K.180, F.181, V.183, P.223 Ligand excluded by PLIP ACT.13: 4 residues within 4Å: Chain A: T.25, E.26, I.27, E.177 Ligand excluded by PLIP ACT.14: 7 residues within 4Å: Chain A: E.18, M.19, T.20, P.21, V.22, R.301, K.328 Ligand excluded by PLIP ACT.15: 3 residues within 4Å: Chain A: N.195, E.197 Chain B: R.31 Ligand excluded by PLIP ACT.16: 4 residues within 4Å: Chain A: D.296, I.297, D.298, G.299 Ligand excluded by PLIP ACT.17: 4 residues within 4Å: Chain A: T.25, A.39, K.156, N.179 Ligand excluded by PLIP ACT.18: 5 residues within 4Å: Chain A: D.296, G.299, V.300, R.301 Ligands: ACT.7 Ligand excluded by PLIP ACT.19: 5 residues within 4Å: Chain A: R.343, H.406, K.407, G.408, E.409 Ligand excluded by PLIP ACT.20: 8 residues within 4Å: Chain A: E.75, S.76, Q.77, E.80, P.82, T.83, Q.84, M.92 Ligand excluded by PLIP ACT.21: 4 residues within 4Å: Chain A: D.69, R.70, F.71, G.89 Ligand excluded by PLIP ACT.22: 8 residues within 4Å: Chain A: P.52, I.100, P.101, C.102, G.103, A.104, D.105, I.140 Ligand excluded by PLIP ACT.23: 4 residues within 4Å: Chain A: L.227, V.230, A.240, E.243 Ligand excluded by PLIP ACT.24: 4 residues within 4Å: Chain A: L.17, D.334, P.335, R.336 Ligand excluded by PLIP ACT.25: 4 residues within 4Å: Chain A: K.341, V.410, V.411, D.412 Ligand excluded by PLIP ACT.26: 7 residues within 4Å: Chain A: H.159, R.327, I.332 Chain B: R.387, S.388 Ligands: ACT.5, ACT.6 Ligand excluded by PLIP ACT.27: 4 residues within 4Å: Chain A: K.56, Q.109, Q.138, D.139 Ligand excluded by PLIP ACT.35: 5 residues within 4Å: Chain A: S.385 Chain B: C.152, V.153, L.154, A.155 Ligand excluded by PLIP ACT.36: 7 residues within 4Å: Chain A: R.387 Chain B: R.327, D.334, R.336, P.337, T.338 Ligands: ACT.57 Ligand excluded by PLIP ACT.37: 8 residues within 4Å: Chain A: S.388, R.418 Chain B: M.34, G.35, H.159, M.160, G.161 Ligands: ACT.57 Ligand excluded by PLIP ACT.38: 7 residues within 4Å: Chain B: P.21, V.22, L.23, G.24, V.300, R.301 Ligands: ACT.49 Ligand excluded by PLIP ACT.39: 6 residues within 4Å: Chain A: L.48, R.141, D.146 Chain B: P.311, V.312 Ligands: MPD.61 Ligand excluded by PLIP ACT.40: 3 residues within 4Å: Chain B: L.6, S.8, F.283 Ligand excluded by PLIP ACT.41: 4 residues within 4Å: Chain B: L.6, F.283, L.288, R.353 Ligand excluded by PLIP ACT.42: 3 residues within 4Å: Chain A: R.31, D.32 Chain B: Q.218 Ligand excluded by PLIP ACT.43: 6 residues within 4Å: Chain B: E.26, R.36, K.180, F.181, V.183, P.223 Ligand excluded by PLIP ACT.44: 4 residues within 4Å: Chain B: T.25, E.26, I.27, E.177 Ligand excluded by PLIP ACT.45: 7 residues within 4Å: Chain B: E.18, M.19, T.20, P.21, V.22, R.301, K.328 Ligand excluded by PLIP ACT.46: 3 residues within 4Å: Chain A: R.31 Chain B: N.195, E.197 Ligand excluded by PLIP ACT.47: 4 residues within 4Å: Chain B: D.296, I.297, D.298, G.299 Ligand excluded by PLIP ACT.48: 4 residues within 4Å: Chain B: T.25, A.39, K.156, N.179 Ligand excluded by PLIP ACT.49: 5 residues within 4Å: Chain B: D.296, G.299, V.300, R.301 Ligands: ACT.38 Ligand excluded by PLIP ACT.50: 5 residues within 4Å: Chain B: R.343, H.406, K.407, G.408, E.409 Ligand excluded by PLIP ACT.51: 8 residues within 4Å: Chain B: E.75, S.76, Q.77, E.80, P.82, T.83, Q.84, M.92 Ligand excluded by PLIP ACT.52: 4 residues within 4Å: Chain B: D.69, R.70, F.71, G.89 Ligand excluded by PLIP ACT.53: 8 residues within 4Å: Chain B: P.52, I.100, P.101, C.102, G.103, A.104, D.105, I.140 Ligand excluded by PLIP ACT.54: 4 residues within 4Å: Chain B: L.227, V.230, A.240, E.243 Ligand excluded by PLIP ACT.55: 4 residues within 4Å: Chain B: L.17, D.334, P.335, R.336 Ligand excluded by PLIP ACT.56: 4 residues within 4Å: Chain B: K.341, V.410, V.411, D.412 Ligand excluded by PLIP ACT.57: 7 residues within 4Å: Chain A: R.387, S.388 Chain B: H.159, R.327, I.332 Ligands: ACT.36, ACT.37 Ligand excluded by PLIP ACT.58: 4 residues within 4Å: Chain B: K.56, Q.109, Q.138, D.139 Ligand excluded by PLIP

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

NA.28: 7 residues within 4Å: Chain A: P.286, G.287, L.288, P.289, P.308, N.310, S.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.287, A:S.313, A:S.313 Water bridges: A:L.288 NA.59: 7 residues within 4Å: Chain B: P.286, G.287, L.288, P.289, P.308, N.310, S.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.287, B:S.313 Water bridges: B:L.288

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

ADP.29: 26 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, D.263, P.289, P.308, G.309, N.310, P.311 Chain B: T.96, G.97, R.141 Ligands: CA.1, CA.2 23 PLIP interactions: 17 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.188, A:D.207, A:D.207, A:S.208, A:S.208, A:N.209, A:G.256, A:V.257, A:S.258, A:S.258, A:S.258, A:G.309, B:R.141 Water bridges: A:E.192, A:E.192, A:N.209, A:N.209, A:N.310, B:T.96, B:T.96, B:T.96, B:G.97, B:G.97 ADP.60: 26 residues within 4Å: Chain A: 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, D.263, P.289, P.308, G.309, N.310, P.311 Ligands: CA.32, CA.33 24 PLIP interactions: 18 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.188, B:E.192, B:D.207, B:S.208, B:S.208, B:N.209, B:G.256, B:V.257, B:S.258, B:S.258, B:S.258, B:G.309, A:R.141 Water bridges: B:E.192, B:E.192, B:N.209, B:N.209, B:D.263, B:N.310, A:T.96, A:T.96, A:T.96, A:G.97, A:G.97

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

MPD.30: 13 residues within 4Å: Chain A: S.208, T.212, P.311, V.312, V.315, R.358 Chain B: L.48, I.147, S.163, G.166, L.167, T.170 Ligands: ACT.8 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.212, A:P.311, A:V.312, B:L.167 Hydrogen bonds: A:R.358, A:R.358 Water bridges: A:S.208 MPD.61: 13 residues within 4Å: Chain A: L.48, I.147, S.163, G.166, L.167, T.170 Chain B: S.208, T.212, P.311, V.312, V.315, R.358 Ligands: ACT.39 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.212, B:P.311, B:V.312, A:L.167 Hydrogen bonds: B:R.358, B:R.358 Water bridges: B:S.208

2 x D8Z: Artemether(Non-covalent)

D8Z.31: 12 residues within 4Å: Chain A: M.9, D.10, F.13, I.14, L.320, P.324, R.336, P.337, I.339, Y.356, M.394, M.414 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.13, A:F.13, A:F.13, A:P.337, A:I.339, A:I.339 D8Z.62: 12 residues within 4Å: Chain B: M.9, D.10, F.13, I.14, L.320, P.324, R.336, P.337, I.339, Y.356, M.394, M.414 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.13, B:F.13, B:F.13, B:P.337, B:I.339, B:I.339 Hydrogen bonds: B:D.10

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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