SMTL ID : 3qel.1 (1 other biounit)

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with ifenprodil

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-FUC.1: 3 residues within 4Å: Chain A: Q.349, N.367, Y.370 No protein-ligand interaction detected (PLIP)

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

NA.2: 3 residues within 4Å: Chain A: Y.106, F.115, D.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.115, A:D.342

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

NAG.3: 3 residues within 4Å: Chain A: N.275, S.277, A.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.275, A:A.278 NAG.4: 1 residues within 4Å: Chain B: N.44 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain B: N.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.311 NAG.7: 1 residues within 4Å: Chain C: N.44 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain C: N.311 No protein-ligand interaction detected (PLIP)

2 x QEL: 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol(Non-covalent)

QEL.6: 15 residues within 4Å: Chain A: Y.87, T.88, R.93, S.110, I.111, L.113 Chain B: A.77, Q.80, I.81, F.84, T.144, Y.145, F.146, P.147, E.206 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.77, B:I.81, B:F.84, A:Y.87, A:L.113 Hydrogen bonds: B:Q.80, B:E.206 Water bridges: B:Y.145 pi-Stacking: B:F.146 QEL.9: 10 residues within 4Å: Chain C: P.48, A.77, Q.80, I.81, F.84, T.144, Y.145, F.146, P.147, E.206 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:P.48, C:A.77, C:I.81, C:F.84, C:F.84 Hydrogen bonds: C:Q.80, C:T.144, C:E.206 Water bridges: C:Y.145 pi-Stacking: C:F.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karakas, E. et al., Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors. Nature (2011)

Release Date

2011-06-15

Peptides

NMDA glutamate receptor subunit: A
Glutamate [NMDA] receptor subunit epsilon-2: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

NMDA glutamate receptor subunit

Glutamate [NMDA] receptor subunit epsilon-2

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