SMTL ID : 6jmv.2 (1 other biounit)

Crystal structure of the GluK3 ligand binding domain complex with SYM and zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.240, H.243 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.240, A:D.240, A:H.243 ZN.3: 1 residues within 4Å: Chain A: H.80 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.80, H2O.3

1 x SYM: 2S,4R-4-METHYLGLUTAMATE(Non-covalent)

SYM.2: 14 residues within 4Å: Chain A: Y.61, P.88, L.89, T.90, R.95, V.137, G.140, A.141, T.142, M.143, N.172, M.188, E.189, Y.215 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.61, A:V.137 Hydrogen bonds: A:T.90, A:A.141, A:T.142, A:T.142, A:E.189, A:E.189 Water bridges: A:V.137, A:V.137, A:E.189, A:E.189 Salt bridges: A:R.95

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

CL.4: 5 residues within 4Å: Chain A: R.31, F.32, I.53, R.54, L.55 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: D.58, K.60, N.71 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: K.21 Ligands: GOL.8 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: K.60, Y.61, G.62, A.63, N.71, V.137, K.138, D.139, G.140 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.61, A:G.62, A:N.71, A:N.71, A:D.139, A:D.139 GOL.7: 7 residues within 4Å: Chain A: L.236, Q.237, D.240, K.241, L.242, H.243 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.237, A:Q.237, A:D.240, A:L.242, A:H.243 GOL.8: 7 residues within 4Å: Chain A: K.21, S.22, D.23, R.24, T.25, L.26 Ligands: CL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.22, A:T.25 GOL.9: 8 residues within 4Å: Chain A: E.13, E.14, N.172, E.173, I.176, T.192, Y.195, I.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.13, A:E.13, A:E.13, A:E.14, A:N.172, A:E.173 Water bridges: A:E.173

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

ACT.10: 4 residues within 4Å: Chain A: D.100, M.221, G.222, R.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.100 Salt bridges: A:R.226 ACT.11: 7 residues within 4Å: Chain A: L.108, S.190, T.191, E.194, Q.205, L.209, K.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.190 Salt bridges: A:K.246 ACT.12: 6 residues within 4Å: Chain A: E.42, I.46, Q.235, L.236, E.239, K.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.235 Salt bridges: A:K.241

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

NA.14: 5 residues within 4Å: Chain A: E.194, Q.198, K.246, E.247, W.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.194, A:Q.198, A:E.247 NA.15: 2 residues within 4Å: Chain A: R.226, D.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.226, A:R.226, A:D.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumari, J. et al., Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery. Sci Rep (2019)

Release Date

2019-07-24

Peptides

Glutamate receptor ionotropic, kainate 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glutamate receptor ionotropic, kainate 3

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