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

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 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: 3 residues within 4Å: Chain A: N.367, S.369, Y.370 No protein-ligand interaction detected (PLIP)

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

NA.2: 2 residues within 4Å: Chain A: F.115, D.342 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.115, A:F.115 Water bridges: A:K.321, A:K.321 NA.4: 4 residues within 4Å: Chain A: V.363, Q.373, N.374, R.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.363, A:N.374 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:T.33 NA.9: 3 residues within 4Å: Chain B: R.298, I.299, Q.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.298

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

NAG.3: 3 residues within 4Å: Chain A: N.275, A.278, V.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.275, A:A.278 NAG.6: 1 residues within 4Å: Chain B: N.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 NAG.7: 2 residues within 4Å: Chain B: N.311, T.313 No protein-ligand interaction detected (PLIP)

1 x 5SM: 5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methyl]pyridazine(Non-covalent)

5SM.8: 14 residues within 4Å: Chain A: A.53, Y.87, T.88, F.91, I.111 Chain B: P.48, I.52, Q.80, I.81, F.84, M.104, A.105, D.106, P.147 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.80, B:Q.80, B:I.81, B:P.147, A:Y.87 pi-Stacking: A:Y.87

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

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