SMTL ID : 3om1.1

Crystal structure of the GluK5 (KA2) ATD dimer at 1.7 Angstrom Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: R.19, S.79, A.147, K.148, D.176, R.178, N.200, S.202, I.203 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 10 residues within 4Å: Chain B: Q.14, R.19, A.147, L.174, D.175, S.177, R.178, N.200, S.202, I.203 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: S.131, L.134, Y.139, P.140, L.158, G.161, F.162, S.165, E.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.140, A:L.158 Water bridges: A:S.131 GOL.9: 7 residues within 4Å: Chain B: L.134, Y.139, P.140, G.161, F.162, S.165, E.167 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.165, B:S.165

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

NAG.4: 8 residues within 4Å: Chain A: N.252, S.254, H.255, P.256, D.337, G.341, R.342, T.355 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.252, A:R.342 Water bridges: A:N.252, A:T.355, A:T.355 NAG.5: 5 residues within 4Å: Chain A: V.262, N.266, R.270, Y.278, G.280 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.278 Hydrogen bonds: A:N.266, A:R.270, A:R.270 NAG.6: 8 residues within 4Å: Chain A: S.4, L.5, K.41, A.42, V.299, R.300, N.303, E.307 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.5, A:A.42 Hydrogen bonds: A:A.42 Water bridges: A:K.41, A:R.300, A:R.300 NAG.7: 4 residues within 4Å: Chain A: D.337, R.342, E.344, N.353 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.342, A:N.353 Water bridges: A:N.353 NAG.10: 9 residues within 4Å: Chain B: N.252, S.254, H.255, P.256, D.337, G.341, R.342, T.355 Ligands: NAG.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.252, B:R.342 NAG.11: 6 residues within 4Å: Chain B: V.262, N.266, R.270, Y.278, P.279, G.280 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.278 Hydrogen bonds: B:N.266, B:R.270 Water bridges: B:Y.278 NAG.12: 7 residues within 4Å: Chain B: L.2, L.5, K.41, A.42, V.299, R.300, N.303 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.5 Hydrogen bonds: B:A.42, B:N.303 NAG.13: 5 residues within 4Å: Chain B: D.337, R.342, E.344, N.353 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.353 Water bridges: B:N.353

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

NA.8: 5 residues within 4Å: Chain A: F.162, S.165, E.167, T.168 Ligands: NA.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.165, A:E.167 NA.14: 5 residues within 4Å: Chain B: F.162, S.165, E.167, T.168 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.162, B:S.165

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
B

Glutamate receptor ionotropic, kainate 5

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