SMTL ID : 3jpw.2 (1 other biounit)

Crystal structure of amino terminal domain of the NMDA receptor subunit NR2B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.43, E.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.43 NAG.2: 2 residues within 4Å: Chain A: D.275, N.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.310 NAG.21: 2 residues within 4Å: Chain B: N.43, E.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.43 NAG.22: 2 residues within 4Å: Chain B: D.275, N.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.310

34 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: M.101, I.102, Q.122, S.229, L.230 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: H.96, S.100, Y.251, R.261 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: E.253, W.254, D.255, Y.256, R.261 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: A.260, R.263 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: G.147, Y.148, Q.149 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Q.149, N.153 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: E.343, R.344 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: G.346, Q.354, K.356 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: M.42, N.43, E.44 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: S.289, C.290, Y.291, N.292 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: N.302 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: L.173, L.174, D.175, Q.188 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: N.214, E.241 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: T.72, D.73, Q.74 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: N.337, K.338 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: S.118, I.119, E.120, Y.325 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: H.29, R.263 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: M.101, I.102, Q.122, S.229, L.230 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: H.96, S.100, Y.251, R.261 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain B: E.253, W.254, D.255, Y.256, R.261 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: A.260, R.263 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: G.147, Y.148, Q.149 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: Q.149, N.153 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain B: E.343, R.344 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: G.346, Q.354, K.356 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: M.42, N.43, E.44 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain B: S.289, C.290, Y.291, N.292 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain B: N.302 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain B: L.173, L.174, D.175, Q.188 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain B: N.214, E.241 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain B: T.72, D.73, Q.74 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain B: N.337, K.338 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain B: S.118, I.119, E.120, Y.325 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain B: H.29, R.263 Ligand excluded by PLIP

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

NA.20: 3 residues within 4Å: Chain A: S.100, F.115, G.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.100 NA.40: 3 residues within 4Å: Chain B: S.100, F.115, G.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karakas, E. et al., Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit. Embo J. (2009)

Release Date

2009-12-08

Peptides

Glutamate [NMDA] receptor subunit epsilon-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate [NMDA] receptor subunit epsilon-2

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