SMTL ID : 3u92.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x KAI: 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE(Non-covalent)

KAI.1: 16 residues within 4Å: Chain A: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, A.141, T.142, M.143, N.171, 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:T.90, A:A.141, A:T.142, A:T.142 Water bridges: A:V.137, A:V.137, A:V.137, A:N.172, A:E.189 Salt bridges: A:R.95 KAI.6: 15 residues within 4Å: Chain B: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, A.141, T.142, N.171, N.172, M.188, E.189, Y.215 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.61, B:V.137 Hydrogen bonds: B:T.90, B:T.90, B:A.141, B:T.142, B:T.142 Water bridges: B:V.137, B:V.137, B:V.137, B:E.189 Salt bridges: B:R.95 KAI.13: 16 residues within 4Å: Chain C: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, A.141, T.142, M.143, N.171, N.172, M.188, E.189, Y.215 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.61, C:V.137 Hydrogen bonds: C:T.90, C:T.90, C:A.141, C:T.142, C:T.142 Water bridges: C:V.137, C:V.137, C:V.137, C:N.172, C:E.189 Salt bridges: C:R.95 KAI.18: 15 residues within 4Å: Chain D: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, A.141, T.142, N.171, N.172, M.188, E.189, Y.215 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.61, D:V.137 Hydrogen bonds: D:T.90, D:T.90, D:A.141, D:T.142, D:T.142 Water bridges: D:V.137, D:V.137, D:V.137, D:E.189 Salt bridges: D:R.95

16 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.194, K.246 Chain C: H.243, I.244, E.247 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Metal complexes: A:E.194, A:E.194, C:H.243, C:E.247, C:E.247 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.4 ZN.4: 1 residues within 4Å: Chain A: H.45 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.45, H2O.8, H2O.8 ZN.7: 4 residues within 4Å: Chain A: H.93, E.96 Chain B: D.240, H.243 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.240, B:D.240, B:H.243, A:H.93, A:E.96 ZN.8: 3 residues within 4Å: Chain B: E.96, D.100, M.221 No protein-ligand interaction detected (PLIP) ZN.9: 4 residues within 4Å: Chain B: E.42, L.236, K.241 Chain D: H.45 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:E.42, H2O.13 ZN.10: 1 residues within 4Å: Chain B: E.238 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.238, B:E.238, H2O.10, H2O.13 ZN.11: 1 residues within 4Å: Chain B: H.80 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.80 ZN.14: 5 residues within 4Å: Chain A: H.243, I.244, 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.15: 1 residues within 4Å: Chain C: H.80 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.80, H2O.18 ZN.16: 1 residues within 4Å: Chain C: H.45 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.45, H2O.22, H2O.22 ZN.19: 4 residues within 4Å: Chain C: H.93, E.96 Chain D: D.240, H.243 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:H.93, C:E.96, D:D.240, D:D.240, D:H.243 ZN.20: 3 residues within 4Å: Chain D: E.96, D.100, M.221 No protein-ligand interaction detected (PLIP) ZN.21: 4 residues within 4Å: Chain B: H.45 Chain D: E.42, L.236, K.241 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.42, D:E.42, H2O.27 ZN.22: 1 residues within 4Å: Chain D: E.238 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.238, D:E.238, H2O.24, H2O.27 ZN.23: 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.5: 3 residues within 4Å: Chain A: R.31, R.54, L.55 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: R.31, F.32, R.54, L.55 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain C: R.31, R.54, L.55 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain D: R.31, F.32, R.54, L.55 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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