SMTL ID : 5ewl.1 (1 other biounit)

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH MK-22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 4 residues within 4Å: Chain A: Q.349, N.367, S.369, Y.370 No protein-ligand interaction detected (PLIP)

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

NA.2: 3 residues within 4Å: Chain A: F.115, D.342, G.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.321, A:D.342 NA.5: 4 residues within 4Å: Chain A: N.28, K.29, H.31, T.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.31 NA.6: 4 residues within 4Å: Chain A: V.363, Q.373, N.374, R.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.373, A:N.374, A:R.376 NA.9: 1 residues within 4Å: Chain B: S.282 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.282 NA.10: 2 residues within 4Å: Chain B: R.298, Q.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.301

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

NAG.3: 4 residues within 4Å: Chain A: N.275, A.278, S.281, V.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.281 Water bridges: A:S.277 NAG.7: 1 residues within 4Å: Chain B: N.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 NAG.8: 1 residues within 4Å: Chain B: N.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.311

1 x 5SL: ~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine(Non-covalent)

5SL.4: 19 residues within 4Å: Chain A: A.53, Y.87, T.88, F.91, R.93, S.110, I.111, L.113 Chain B: P.48, E.76, A.77, Q.80, I.81, F.84, Y.145, F.146, P.147, T.203, E.206 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:P.48, B:P.48, B:A.77, B:I.81, B:F.84, B:F.84, B:P.147, A:A.53, A:Y.87, A:Y.87, A:F.91, A:L.113, A:L.113 Hydrogen bonds: B:E.206, A:R.93, A:S.110 Water bridges: B:T.203 pi-Stacking: B:F.146 pi-Cation interactions: A:R.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroebel, D. et al., A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists. Mol.Pharmacol. (2016)

Release Date

2016-03-02

Peptides

NMDA glutamate receptor subunit: A
Glutamate receptor ionotropic, NMDA 2B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NMDA glutamate receptor subunit

Glutamate receptor ionotropic, NMDA 2B

Related Entries With Identical Sequence