SMTL ID : 3om0.1

Crystal structure of the GluK5 (KA2) ATD crystallographic dimer at 1.4 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: Q.14, T.15, N.200, A.201, S.202, I.203 Ligands: GOL.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 7 residues within 4Å: Chain B: Q.14, T.15, N.200, A.201, S.202, I.203 Ligands: GOL.16 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 8 residues within 4Å: Chain A: N.252, S.254, H.255, P.256, G.341, R.342, T.355 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.252 NAG.3: 6 residues within 4Å: Chain A: V.262, N.266, R.270, A.275, Y.278, G.280 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.278 Hydrogen bonds: A:N.266, A:R.270 Water bridges: A:A.275, A:Y.278 NAG.4: 10 residues within 4Å: Chain A: L.2, L.5, P.39, A.40, K.41, A.42, V.299, R.300, N.303, I.308 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.42 Hydrogen bonds: A:A.42, A:R.300, A:N.303 Water bridges: A:L.2, A:N.303 NAG.5: 4 residues within 4Å: Chain A: D.337, R.342, E.344, N.353 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.353 NAG.11: 8 residues within 4Å: Chain B: N.252, S.254, H.255, P.256, G.341, R.342, T.355 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.252 NAG.12: 6 residues within 4Å: Chain B: V.262, N.266, R.270, A.275, Y.278, G.280 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.278 Hydrogen bonds: B:N.266, B:R.270 Water bridges: B:A.275, B:Y.278 NAG.13: 10 residues within 4Å: Chain B: L.2, L.5, P.39, A.40, K.41, A.42, V.299, R.300, N.303, I.308 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.42 Hydrogen bonds: B:A.42, B:R.300, B:N.303 Water bridges: B:L.2, B:N.303 NAG.14: 4 residues within 4Å: Chain B: D.337, R.342, E.344, N.353 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.353

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: F.251, N.252, T.253, S.254, R.357 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.251, A:F.251, A:T.253 GOL.7: 9 residues within 4Å: Chain A: T.15, C.17, G.18, R.19, I.232, W.269, P.279, A.282 Ligands: NAG-NAG-BMA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18 Water bridges: A:C.17 GOL.8: 8 residues within 4Å: Chain A: F.137, K.222, S.242, S.243, N.244, L.246, E.360, I.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.243, A:E.360 GOL.15: 6 residues within 4Å: Chain B: F.251, N.252, T.253, S.254, R.357 Ligands: NAG.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.251, B:F.251, B:T.253 GOL.16: 9 residues within 4Å: Chain B: T.15, C.17, G.18, R.19, I.232, W.269, P.279, A.282 Ligands: NAG-NAG-BMA.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.18 Water bridges: B:C.17 GOL.17: 8 residues within 4Å: Chain B: F.137, K.222, S.242, S.243, N.244, L.246, E.360, I.369 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.243

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

ACT.9: 6 residues within 4Å: Chain A: E.93, K.94, S.317, A.318, N.319, I.320 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.320 Hydrogen bonds: A:E.93, A:N.319 Salt bridges: A:K.94 ACT.18: 6 residues within 4Å: Chain B: E.93, K.94, S.317, A.318, N.319, I.320 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.320 Hydrogen bonds: B:N.319 Salt bridges: B:K.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, J. et al., Crystal Structures of the Glutamate Receptor Ion Channel GluK3 and GluK5 Amino-Terminal Domains. J.Mol.Biol. (2010)

Release Date

2010-11-03

Peptides

Glutamate receptor, ionotropic kainate 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor, ionotropic kainate 5

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