Research workbench
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2B in apo closed state
Analyse Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TPZ
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NMDA glutamate receptor subunit; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- Q91977, Q00960
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NMDA glutamate receptor subunit | protein | 354 | 37% helix, 21% strand | Q91977 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 352 | 32% helix, 22% strand | Q00960 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.76 | 0.81 | 71 | empty |
| 2 | 180 | 0.68 | 0.87 | 42 | empty |
| 3 | 78 | 0.59 | 0.88 | 32 | empty |
| 4 | 240 | 0.55 | 0.78 | 40 | empty |
| 5 | 50 | 0.52 | 0.87 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 1038 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5TPZ · Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B… · 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 D against A, TM-score 0.98
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 Q91977
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 5TPZ · PDBe 5TPZ · UniProt Q91977 · UniProt Q00960
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