SMTL ID : 3u93.1

Crystal structure of the GluK3 ligand binding domain complex with glutamate and zinc: P2221 form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 13 residues within 4Å: Chain A: Y.61, P.88, L.89, T.90, R.95, V.137, G.140, A.141, T.142, N.172, M.188, E.189, Y.215 14 PLIP interactions: 12 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:T.90, A:T.90, A:A.141, A:T.142, A:T.142, A:E.189, E.1, E.1 Water bridges: A:V.137, A:V.137, A:V.137, A:E.189 Salt bridges: A:R.95 GLU.3: 14 residues within 4Å: Chain B: 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 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:P.88, B:T.90, B:T.90, B:A.141, B:T.142, B:T.142, E.3 Water bridges: B:V.137, B:V.137, B:V.137, B:E.189, B:E.189 Salt bridges: B:R.95 GLU.10: 13 residues within 4Å: Chain C: Y.61, P.88, L.89, T.90, R.95, V.137, G.140, A.141, T.142, N.172, M.188, E.189, Y.215 15 PLIP interactions: 13 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:Y.61 Hydrogen bonds: C:T.90, C:T.90, C:A.141, C:T.142, C:T.142, C:E.189, E.10, E.10 Water bridges: C:V.137, C:V.137, C:V.137, C:E.189, C:E.189 Salt bridges: C:R.95 GLU.12: 14 residues within 4Å: Chain D: 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 14 PLIP interactions: 1 Ligand-Ligand interactions, 13 interactions with chain D Hydrogen bonds: E.12, D:P.88, D:T.90, D:T.90, D:A.141, D:T.142, D:T.142 Hydrophobic interactions: D:Y.61 Water bridges: D:V.137, D:V.137, D:V.137, D:E.189, D:E.189 Salt bridges: D:R.95

10 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.243, E.247 Chain C: E.194, K.246 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Metal complexes: C:E.194, C:E.194, A:H.243, A:E.247, A:E.247 ZN.4: 4 residues within 4Å: Chain A: H.93, E.96 Chain B: D.240, H.243 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.93, A:E.96, B:D.240, B:D.240, B:H.243 ZN.5: 2 residues within 4Å: Chain B: H.93, K.97 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.93 ZN.6: 4 residues within 4Å: Chain B: E.42, L.236, K.241 Chain D: H.45 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:E.42, B:E.42, D:H.45, H2O.8 ZN.7: 1 residues within 4Å: Chain B: H.80 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.80 ZN.11: 4 residues within 4Å: Chain A: E.194, K.246 Chain C: H.243, E.247 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.243, C:E.247, C:E.247, A:E.194, A:E.194 ZN.13: 4 residues within 4Å: Chain C: H.93, E.96 Chain D: D.240, H.243 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Metal complexes: D:D.240, D:D.240, D:H.243, C:H.93, C:E.96 ZN.14: 2 residues within 4Å: Chain D: H.93, K.97 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.93 ZN.15: 4 residues within 4Å: Chain B: H.45 Chain D: E.42, L.236, K.241 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:E.42, D:E.42, B:H.45, H2O.16 ZN.16: 1 residues within 4Å: Chain D: H.80 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.80

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

CL.8: 4 residues within 4Å: Chain B: R.31, F.32, R.54, L.55 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: R.20, R.24, L.26 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain D: R.31, F.32, R.54, L.55 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain D: R.20, R.24, L.26 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Veran, J. et al., Zinc Potentiates GluK3 Glutamate Receptor Function by Stabilizing the Ligand Binding Domain Dimer Interface. Neuron (2012)

Release Date

2012-09-26

Peptides

Glutamate receptor, ionotropic kainate 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glutamate receptor, ionotropic kainate 3

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