SMTL ID : 5tq0.1

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in the presence of EDTA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: K.273, N.274 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.274 NAG.2: 4 residues within 4Å: Chain A: N.366, Y.369, I.371 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.366

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: T.12, K.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.13 GOL.4: 6 residues within 4Å: Chain A: H.123, L.126, K.156, N.339, R.344, K.345 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.123, A:K.156, A:N.339

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: H.15, K.273, N.274, E.275, S.276 Ligands: NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.275, A:S.276, A:S.276 Salt bridges: A:H.15 SO4.6: 2 residues within 4Å: Chain A: R.335 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.335 SO4.7: 3 residues within 4Å: Chain A: S.222, E.223, R.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.223 SO4.8: 3 residues within 4Å: Chain A: T.199, K.200, N.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.200, A:N.201 SO4.9: 5 residues within 4Å: Chain A: T.310, N.311, I.312 Chain B: D.72, Q.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.311, A:I.312 SO4.10: 4 residues within 4Å: Chain B: R.211, P.240, S.241, R.337 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.241 Salt bridges: B:R.211, B:R.337 SO4.11: 4 residues within 4Å: Chain B: G.146, Y.147, R.148, D.149 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.146, B:G.146, B:Y.147, B:R.148, B:D.149 Salt bridges: B:R.148 SO4.12: 2 residues within 4Å: Chain B: T.300, H.302 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.300, B:T.300 SO4.13: 2 residues within 4Å: Chain B: R.211, S.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.212 Salt bridges: B:R.211 SO4.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.16: 2 residues within 4Å: Chain D: R.108, D.170 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.108 SO4.17: 4 residues within 4Å: Chain D: E.154, R.155, Q.156, N.157 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.156, D:N.157 Salt bridges: D:R.155

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.15: 9 residues within 4Å: Chain C: F.172, P.173, T.182, L.183, S.184 Chain D: L.160, S.162, S.176, T.178 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.172, C:T.182, D:S.162, D:T.178 Hydrogen bonds: D:S.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romero-Hernandez, A. et al., Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain. Neuron (2016)

Release Date

2016-12-14

Peptides

NMDA glutamate receptor subunit: A
Glutamate receptor ionotropic, NMDA 2A: B
FAB, HEAVY CHAIN: C
FAB, LIGHT CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

NMDA glutamate receptor subunit

Glutamate receptor ionotropic, NMDA 2A

FAB, HEAVY CHAIN

FAB, LIGHT CHAIN

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