SMTL ID : 4pe5.1

Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.96 Å

Oligo State

hetero-2-2-mer

Ligands

3 x NAG- NAG- BMA- MAN: 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.1: 4 residues within 4Å: Chain A: N.346, H.349, V.350, I.351 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.349 NAG-NAG-BMA-MAN.5: 2 residues within 4Å: Chain C: N.418, H.427 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.6: 2 residues within 4Å: Chain D: P.655, N.656 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.2: 2 residues within 4Å: Chain A: N.181, T.183 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-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-MAN.3: 2 residues within 4Å: Chain B: P.655, N.656 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 3 residues within 4Å: Chain C: N.346, H.349, I.351 No protein-ligand interaction detected (PLIP)

84 x W: TUNGSTEN ION(Non-functional Binders)(Non-covalent)

W.7: 6 residues within 4Å: Ligands: W.8, W.11, W.12, W.16, W.51, W.52 Ligand excluded by PLIP W.8: 7 residues within 4Å: Ligands: W.7, W.9, W.13, W.16, W.43, W.50, W.51 Ligand excluded by PLIP W.9: 8 residues within 4Å: Ligands: W.8, W.10, W.11, W.13, W.43, W.48, W.49, W.51 Ligand excluded by PLIP W.10: 4 residues within 4Å: Ligands: W.9, W.11, W.17, W.18 Ligand excluded by PLIP W.11: 7 residues within 4Å: Ligands: W.7, W.9, W.10, W.12, W.48, W.51, W.52 Ligand excluded by PLIP W.12: 4 residues within 4Å: Ligands: W.7, W.11, W.15, W.18 Ligand excluded by PLIP W.13: 4 residues within 4Å: Ligands: W.8, W.9, W.14, W.17 Ligand excluded by PLIP W.14: 4 residues within 4Å: Ligands: W.13, W.15, W.16, W.17 Ligand excluded by PLIP W.15: 4 residues within 4Å: Ligands: W.12, W.14, W.16, W.18 Ligand excluded by PLIP W.16: 4 residues within 4Å: Ligands: W.7, W.8, W.14, W.15 Ligand excluded by PLIP W.17: 4 residues within 4Å: Ligands: W.10, W.13, W.14, W.18 Ligand excluded by PLIP W.18: 4 residues within 4Å: Ligands: W.10, W.12, W.15, W.17 Ligand excluded by PLIP W.19: 4 residues within 4Å: Ligands: W.20, W.23, W.24, W.28 Ligand excluded by PLIP W.20: 4 residues within 4Å: Ligands: W.19, W.21, W.25, W.28 Ligand excluded by PLIP W.21: 4 residues within 4Å: Ligands: W.20, W.22, W.23, W.25 Ligand excluded by PLIP W.22: 4 residues within 4Å: Ligands: W.21, W.23, W.29, W.30 Ligand excluded by PLIP W.23: 4 residues within 4Å: Ligands: W.19, W.21, W.22, W.24 Ligand excluded by PLIP W.24: 4 residues within 4Å: Ligands: W.19, W.23, W.27, W.30 Ligand excluded by PLIP W.25: 4 residues within 4Å: Ligands: W.20, W.21, W.26, W.29 Ligand excluded by PLIP W.26: 4 residues within 4Å: Ligands: W.25, W.27, W.28, W.29 Ligand excluded by PLIP W.27: 4 residues within 4Å: Ligands: W.24, W.26, W.28, W.30 Ligand excluded by PLIP W.28: 4 residues within 4Å: Ligands: W.19, W.20, W.26, W.27 Ligand excluded by PLIP W.29: 4 residues within 4Å: Ligands: W.22, W.25, W.26, W.30 Ligand excluded by PLIP W.30: 4 residues within 4Å: Ligands: W.22, W.24, W.27, W.29 Ligand excluded by PLIP W.31: 4 residues within 4Å: Ligands: W.32, W.35, W.36, W.40 Ligand excluded by PLIP W.32: 4 residues within 4Å: Ligands: W.31, W.33, W.37, W.40 Ligand excluded by PLIP W.33: 4 residues within 4Å: Ligands: W.32, W.34, W.35, W.37 Ligand excluded by PLIP W.34: 4 residues within 4Å: Ligands: W.33, W.35, W.41, W.42 Ligand excluded by PLIP W.35: 4 residues within 4Å: Ligands: W.31, W.33, W.34, W.36 Ligand excluded by PLIP W.36: 4 residues within 4Å: Ligands: W.31, W.35, W.39, W.42 Ligand excluded by PLIP W.37: 4 residues within 4Å: Ligands: W.32, W.33, W.38, W.41 Ligand excluded by PLIP W.38: 4 residues within 4Å: Ligands: W.37, W.39, W.40, W.41 Ligand excluded by PLIP W.39: 4 residues within 4Å: Ligands: W.36, W.38, W.40, W.42 Ligand excluded by PLIP W.40: 4 residues within 4Å: Ligands: W.31, W.32, W.38, W.39 Ligand excluded by PLIP W.41: 4 residues within 4Å: Ligands: W.34, W.37, W.38, W.42 Ligand excluded by PLIP W.42: 4 residues within 4Å: Ligands: W.34, W.36, W.39, W.41 Ligand excluded by PLIP W.43: 6 residues within 4Å: Ligands: W.8, W.9, W.49, W.50, W.51, W.53 Ligand excluded by PLIP W.48: 6 residues within 4Å: Ligands: W.9, W.11, W.49, W.51, W.52, W.56 Ligand excluded by PLIP W.49: 5 residues within 4Å: Ligands: W.9, W.43, W.48, W.53, W.56 Ligand excluded by PLIP W.50: 5 residues within 4Å: Ligands: W.8, W.43, W.51, W.57, W.58 Ligand excluded by PLIP W.51: 8 residues within 4Å: Ligands: W.7, W.8, W.9, W.11, W.43, W.48, W.50, W.52 Ligand excluded by PLIP W.52: 6 residues within 4Å: Ligands: W.7, W.11, W.48, W.51, W.55, W.58 Ligand excluded by PLIP W.53: 4 residues within 4Å: Ligands: W.43, W.49, W.54, W.57 Ligand excluded by PLIP W.54: 4 residues within 4Å: Ligands: W.53, W.55, W.56, W.57 Ligand excluded by PLIP W.55: 4 residues within 4Å: Ligands: W.52, W.54, W.56, W.58 Ligand excluded by PLIP W.56: 4 residues within 4Å: Ligands: W.48, W.49, W.54, W.55 Ligand excluded by PLIP W.57: 4 residues within 4Å: Ligands: W.50, W.53, W.54, W.58 Ligand excluded by PLIP W.58: 4 residues within 4Å: Ligands: W.50, W.52, W.55, W.57 Ligand excluded by PLIP W.63: 4 residues within 4Å: Ligands: W.64, W.67, W.68, W.72 Ligand excluded by PLIP W.64: 4 residues within 4Å: Ligands: W.63, W.65, W.69, W.72 Ligand excluded by PLIP W.65: 4 residues within 4Å: Ligands: W.64, W.66, W.67, W.69 Ligand excluded by PLIP W.66: 4 residues within 4Å: Ligands: W.65, W.67, W.73, W.74 Ligand excluded by PLIP W.67: 4 residues within 4Å: Ligands: W.63, W.65, W.66, W.68 Ligand excluded by PLIP W.68: 4 residues within 4Å: Ligands: W.63, W.67, W.71, W.74 Ligand excluded by PLIP W.69: 4 residues within 4Å: Ligands: W.64, W.65, W.70, W.73 Ligand excluded by PLIP W.70: 4 residues within 4Å: Ligands: W.69, W.71, W.72, W.73 Ligand excluded by PLIP W.71: 4 residues within 4Å: Ligands: W.68, W.70, W.72, W.74 Ligand excluded by PLIP W.72: 4 residues within 4Å: Ligands: W.63, W.64, W.70, W.71 Ligand excluded by PLIP W.73: 4 residues within 4Å: Ligands: W.66, W.69, W.70, W.74 Ligand excluded by PLIP W.74: 4 residues within 4Å: Ligands: W.66, W.68, W.71, W.73 Ligand excluded by PLIP W.75: 4 residues within 4Å: Ligands: W.76, W.79, W.80, W.84 Ligand excluded by PLIP W.76: 4 residues within 4Å: Ligands: W.75, W.77, W.81, W.84 Ligand excluded by PLIP W.77: 4 residues within 4Å: Ligands: W.76, W.78, W.79, W.81 Ligand excluded by PLIP W.78: 4 residues within 4Å: Ligands: W.77, W.79, W.85, W.86 Ligand excluded by PLIP W.79: 4 residues within 4Å: Ligands: W.75, W.77, W.78, W.80 Ligand excluded by PLIP W.80: 4 residues within 4Å: Ligands: W.75, W.79, W.83, W.86 Ligand excluded by PLIP W.81: 4 residues within 4Å: Ligands: W.76, W.77, W.82, W.85 Ligand excluded by PLIP W.82: 5 residues within 4Å: Ligands: W.81, W.83, W.84, W.85, W.97 Ligand excluded by PLIP W.83: 6 residues within 4Å: Chain C: W.34 Ligands: W.80, W.82, W.84, W.86, W.93 Ligand excluded by PLIP W.84: 4 residues within 4Å: Ligands: W.75, W.76, W.82, W.83 Ligand excluded by PLIP W.85: 6 residues within 4Å: Ligands: W.78, W.81, W.82, W.86, W.90, W.97 Ligand excluded by PLIP W.86: 6 residues within 4Å: Ligands: W.78, W.80, W.83, W.85, W.89, W.90 Ligand excluded by PLIP W.87: 4 residues within 4Å: Ligands: W.88, W.91, W.92, W.96 Ligand excluded by PLIP W.88: 4 residues within 4Å: Ligands: W.87, W.89, W.93, W.96 Ligand excluded by PLIP W.89: 5 residues within 4Å: Ligands: W.86, W.88, W.90, W.91, W.93 Ligand excluded by PLIP W.90: 6 residues within 4Å: Ligands: W.85, W.86, W.89, W.91, W.97, W.98 Ligand excluded by PLIP W.91: 4 residues within 4Å: Ligands: W.87, W.89, W.90, W.92 Ligand excluded by PLIP W.92: 4 residues within 4Å: Ligands: W.87, W.91, W.95, W.98 Ligand excluded by PLIP W.93: 5 residues within 4Å: Ligands: W.83, W.88, W.89, W.94, W.97 Ligand excluded by PLIP W.94: 4 residues within 4Å: Ligands: W.93, W.95, W.96, W.97 Ligand excluded by PLIP W.95: 4 residues within 4Å: Ligands: W.92, W.94, W.96, W.98 Ligand excluded by PLIP W.96: 4 residues within 4Å: Ligands: W.87, W.88, W.94, W.95 Ligand excluded by PLIP W.97: 6 residues within 4Å: Ligands: W.82, W.85, W.90, W.93, W.94, W.98 Ligand excluded by PLIP W.98: 4 residues within 4Å: Ligands: W.90, W.92, W.95, W.97 Ligand excluded by PLIP

2 x GLY: GLYCINE(Non-covalent)

GLY.44: 9 residues within 4Å: Chain A: F.462, P.494, L.495, T.496, R.501, S.666, W.709, D.710, F.736 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.496, A:S.666, A:S.666, A:D.710 Salt bridges: A:R.501 GLY.100: 9 residues within 4Å: Chain C: F.462, P.494, L.495, T.496, R.501, S.666, W.709, D.710, F.736 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.494, C:T.496, C:S.666, C:S.666 Salt bridges: C:R.501

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

NAG.45: 3 residues within 4Å: Chain A: N.251, N.254, V.312 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.312 Hydrogen bonds: A:N.254 NAG.46: 2 residues within 4Å: Chain A: N.278, T.280 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.280 NAG.47: 1 residues within 4Å: Chain A: N.418 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.392, A:N.418 NAG.59: 1 residues within 4Å: Chain B: N.48 No protein-ligand interaction detected (PLIP) NAG.60: 1 residues within 4Å: Chain B: N.315 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.315 NAG.101: 1 residues within 4Å: Chain C: N.278 No protein-ligand interaction detected (PLIP) NAG.102: 1 residues within 4Å: Chain D: N.48 No protein-ligand interaction detected (PLIP) NAG.103: 1 residues within 4Å: Chain D: N.315 No protein-ligand interaction detected (PLIP)

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

QEL.61: 14 residues within 4Å: Chain A: Y.87, T.88, R.93, S.110, I.111, L.113 Chain B: A.81, Q.84, I.85, F.88, Y.149, F.150, P.151, E.210 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.81, B:I.85, B:F.88, B:F.88, A:Y.87, A:Y.87, A:L.113, A:L.113 Hydrogen bonds: B:Q.84, B:E.210 pi-Stacking: B:F.150 QEL.99: 13 residues within 4Å: Chain C: Y.87, T.88, R.93, S.110, I.111, L.113 Chain D: A.81, Q.84, I.85, F.88, F.150, P.151, E.210 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.81, D:I.85, D:F.88, D:F.88, C:Y.87, C:Y.87, C:L.113, C:L.113 Hydrogen bonds: D:Q.84, D:E.210 pi-Stacking: D:F.150

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.62: 11 residues within 4Å: Chain B: H.454, S.480, L.481, T.482, R.487, G.657, S.658, T.659, Y.699, D.700, Y.730 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.699 Hydrogen bonds: B:S.480, B:T.482, B:T.482, B:S.658, B:S.658, B:T.659, B:T.659, B:D.700, B:D.700, B:Y.730, E.62 Salt bridges: B:H.454, B:R.487 GLU.104: 11 residues within 4Å: Chain D: H.454, S.480, L.481, T.482, R.487, G.657, S.658, T.659, Y.699, D.700, Y.730 12 PLIP interactions: 11 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.699 Hydrogen bonds: D:T.482, D:T.482, D:T.482, D:S.658, D:S.658, D:T.659, D:D.700, D:D.700, E.104 Salt bridges: D:H.454, D:R.487

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karakas, E. et al., Crystal structure of a heterotetrameric NMDA receptor ion channel. Science (2014)

Release Date

2014-06-04

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2B