SMTL ID : 6hso.1

Crystal structure of the ternary complex of GephE-ADP-Glycine receptor derived peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-2-4-mer

Ligands

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

MPD.1: 6 residues within 4Å: Chain A: R.387, N.390, L.419 Chain D: H.159, R.327, T.338 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.419, D:H.159 Hydrogen bonds: A:R.387, A:R.387, A:N.390, D:R.327, D:R.327 Water bridges: A:L.419, D:T.338 MPD.3: 10 residues within 4Å: Chain A: L.419 Chain D: H.220, N.319, V.323, P.324, R.327, P.337, M.414, V.415, I.416 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.324, D:I.416 Hydrogen bonds: D:N.319 Water bridges: D:T.338 MPD.14: 6 residues within 4Å: Chain A: H.159, R.327, T.338 Chain D: R.387, N.390, L.419 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.419, A:H.159 Hydrogen bonds: D:R.387, D:R.387, D:N.390, A:R.327, A:R.327 MPD.16: 10 residues within 4Å: Chain A: H.220, N.319, V.323, P.324, R.327, P.337, M.414, V.415, I.416 Chain D: L.419 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.324, A:I.416 Hydrogen bonds: A:N.319 Water bridges: A:T.338

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

ACT.2: 3 residues within 4Å: Chain A: R.358 Chain D: S.163, L.167 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.212, A:T.212, A:R.358 Salt bridges: A:R.358 ACT.4: 5 residues within 4Å: Chain A: W.363, V.415, G.417, L.419 Ligands: ACT.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.415 Hydrogen bonds: A:L.419 ACT.5: 3 residues within 4Å: Chain A: C.152, V.153 Chain D: S.385 No protein-ligand interaction detected (PLIP) ACT.6: 5 residues within 4Å: Chain A: S.388 Chain D: G.35, H.159, M.160, G.161 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Water bridges: A:S.388, A:S.388, A:S.388, A:R.418 Salt bridges: D:H.159 ACT.7: 3 residues within 4Å: Chain A: L.383, M.384, S.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.384 ACT.8: 2 residues within 4Å: Chain A: N.195, E.197 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.195 Hydrogen bonds: A:E.197 ACT.15: 3 residues within 4Å: Chain A: S.163, L.167 Chain D: R.358 3 PLIP interactions: 3 interactions with chain D Water bridges: D:T.212, D:R.358 Salt bridges: D:R.358 ACT.17: 5 residues within 4Å: Chain D: W.363, V.415, G.417, L.419 Ligands: ACT.4 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.415 Hydrogen bonds: D:L.419 ACT.18: 3 residues within 4Å: Chain A: S.385 Chain D: C.152, V.153 No protein-ligand interaction detected (PLIP) ACT.19: 5 residues within 4Å: Chain A: G.35, H.159, M.160, G.161 Chain D: S.388 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Water bridges: D:S.388, D:S.388, D:S.388, D:R.418, D:L.419 Salt bridges: A:H.159 ACT.20: 3 residues within 4Å: Chain D: L.383, M.384, S.385 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.383, D:M.384 ACT.21: 2 residues within 4Å: Chain D: N.195, E.197 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.195 Hydrogen bonds: D:E.197

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: E.192 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: S.258, D.263 Ligands: ADP.11 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.263, A:D.263, H2O.10, H2O.23 MG.22: 2 residues within 4Å: Chain D: E.192 Ligands: ADP.24 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain D: S.258, D.263 Ligands: ADP.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.263, D:D.263, H2O.8, H2O.26

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

ADP.11: 21 residues within 4Å: Chain A: S.188, E.192, L.193, I.205, R.206, D.207, S.208, N.209, G.255, G.256, V.257, S.258, D.263, P.308, G.309, N.310, P.311 Chain D: T.96, G.97 Ligands: MG.9, MG.10 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.188, A:E.192, A:D.207, A:S.208, A:N.209, A:G.256, A:V.257, A:S.258, A:S.258, A:S.258, A:G.309 Water bridges: A:T.189, A:E.192, A:E.192, A:N.209, A:N.209, A:S.258, A:S.258, A:D.263, A:D.263, A:N.310, A:N.310, A:N.310, D:S.54, D:R.141 ADP.24: 21 residues within 4Å: Chain A: T.96, G.97 Chain D: S.188, E.192, L.193, I.205, R.206, D.207, S.208, N.209, G.255, G.256, V.257, S.258, D.263, P.308, G.309, N.310, P.311 Ligands: MG.22, MG.23 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:S.188, D:D.207, D:D.207, D:S.208, D:N.209, D:G.256, D:V.257, D:S.258, D:S.258, D:S.258, D:G.309 Water bridges: D:E.192, D:N.209, D:N.209, D:S.258, D:N.310, D:N.310, D:N.310, A:S.54, A:T.96, A:T.96, A:R.141

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

PO4.12: 6 residues within 4Å: Chain A: V.183, S.246, R.247, A.248, D.249, K.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.247, A:R.247, A:D.249 Water bridges: A:K.302 Salt bridges: A:K.302 PO4.25: 6 residues within 4Å: Chain D: V.183, S.246, R.247, A.248, D.249, K.302 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.247, D:R.247, D:D.249 Water bridges: D:D.249, D:K.302 Salt bridges: D:K.302

2 x 3F7: 1,1'-benzene-1,4-diylbis(1H-pyrrole-2,5-dione)(Covalent)

3F7.13: 6 residues within 4Å: Chain A: R.343, H.406, K.407, E.409 Chain B: C.11 Chain C: C.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.406 Hydrogen bonds: A:R.343, A:H.406 3F7.26: 6 residues within 4Å: Chain D: R.343, H.406, K.407, E.409 Chain E: C.11 Chain F: C.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:H.406 Hydrogen bonds: D:R.343

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: AD
Glycine receptor beta subunit derived peptide: BCEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
D

C
I

E
D

F
I

Gephyrin

Glycine receptor beta subunit derived peptide

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