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

Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit NR2B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.43 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: N.310, T.312 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.312 Hydrogen bonds: A:N.310 NAG.14: 1 residues within 4Å: Chain B: N.43 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain B: N.310, T.312 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.312 Hydrogen bonds: B:N.310

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

CL.3: 5 residues within 4Å: Chain A: I.102, Q.122, S.229, L.230 Ligands: NA.8 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: H.29, R.263 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: G.147, Y.148, Q.149, D.150 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: V.345, G.346 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: T.72, D.73, Q.74 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: I.102, Q.122, S.229, L.230 Ligands: NA.21 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: H.29, R.263 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: G.147, Y.148, Q.149, D.150 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: V.345, G.346 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: T.72, D.73, Q.74 Ligand excluded by PLIP

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

NA.8: 5 residues within 4Å: Chain A: S.100, F.115, G.116, P.117 Ligands: CL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.100 NA.21: 5 residues within 4Å: Chain B: S.100, F.115, G.116, P.117 Ligands: CL.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.100

10 x ZN: ZINC ION(Non-covalent)

ZN.9: 2 residues within 4Å: Chain A: H.96, E.253 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.96, A:E.253 ZN.10: 2 residues within 4Å: Chain A: H.328, D.350 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.328, A:D.350, A:D.350 ZN.11: 2 residues within 4Å: Chain A: H.29, E.314 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.29, A:E.314 ZN.12: 2 residues within 4Å: Chain A: E.131, E.132 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.131, A:E.132 ZN.13: 1 residues within 4Å: Chain A: H.280 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.280 ZN.22: 2 residues within 4Å: Chain B: H.96, E.253 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.96, B:E.253 ZN.23: 2 residues within 4Å: Chain B: H.328, D.350 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.328, B:D.350, B:D.350 ZN.24: 2 residues within 4Å: Chain B: H.29, E.314 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.29, B:E.314 ZN.25: 2 residues within 4Å: Chain B: E.131, E.132 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.131, B:E.132 ZN.26: 1 residues within 4Å: Chain B: H.280 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.280

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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