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Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2A in the presence of edta
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
- 5TQ0
- Type
- protein
- Length
- 1,118 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NMDA glutamate receptor subunit; Glutamate receptor ionotropic, NMDA 2A; Fab, heavy…
- UniProt
- Q91977, Q00959
- Ligands
- NAG, SO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NMDA glutamate receptor subunit | protein | 364 | 36% helix, 24% strand | Q91977 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 338 | 31% helix, 20% strand | Q00959 |
| H | Fab, heavy chain | protein | 212 | 3% helix, 55% strand | — |
| L | Fab, light chain | protein | 204 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, L
- GOL · Glycerol · additive · 2 copies · chains A
- IPA · Isopropyl alcohol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.78 | 0.80 | 111 | SO4 |
| 2 | 456 | 0.63 | 0.76 | 49 | empty |
| 3 | 79 | 0.59 | 0.88 | 27 | empty |
| 4 | 461 | 0.57 | 0.74 | 51 | empty |
| 5 | 108 | 0.48 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1525 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1220 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 472 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 201 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 161 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5TQ0 · Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00959 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q00959) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q00959
- Elsewhere: RCSB PDB 5TQ0 · PDBe 5TQ0 · UniProt Q91977 · UniProt Q00959
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