MolNFT v1 · #135137 · protein
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2A in the presence of edta
5TQ0 · NMDA glutamate receptor subunit: “Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2A in the presence of…”. X-ray diffraction, 2 ligands (NAG, SO4), 10 pockets (best druggability 0.78). MolNFT…
- 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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