Research workbench
Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit NR2B
Analyse Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JPY
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate [NMDA] receptor subunit epsilon-2
- UniProt
- Q00960
- Ligands
- NAG, ZN, NA, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate [NMDA] receptor subunit epsilon-2 | protein | 358 | 31% helix, 22% strand | Q00960 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 5 copies · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.67 | 0.88 | 30 | CL, NA |
| 2 | 147 | 0.50 | 0.79 | 22 | CL |
| 3 | 52 | 0.33 | 0.77 | 12 | empty |
| 4 | 56 | 0.29 | 0.75 | 12 | empty |
Modifications
Observed in the structure: 2 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 3JPY · Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain A against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 3JPY · PDBe 3JPY · UniProt Q00960
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