MolNFT v1 · #187349 · protein
Glycine and glutamate bound GLUN1A-GLUN2B NMDA receptors in non-active 1 conformation at 2.97 ångström resolution
7SAA · Glutamate receptor ionotropic, NMDA 1: “Glycine and glutamate bound GLUN1A-GLUN2B NMDA receptors in non-active 1 conformation at 2.97 ångström…”. Electron microscopy, 3 ligands (GLY, GLU, NAG), 20 pockets (best druggability 0.84).…
- PDB
- 7SAA
- Type
- protein
- Length
- 3,160 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- P35439, Q00960
- Ligands
- GLY, GLU, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 795 | 38% helix, 18% strand | P35439 |
| B, D | Glutamate receptor ionotropic, NMDA 2B | protein | 785 | 39% helix, 18% strand | Q00960 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, C
- GLU · Glutamic acid · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.84 | 0.93 | 44 | empty |
| 2 | 796 | 0.83 | 0.86 | 95 | empty |
| 3 | 988 | 0.83 | 0.84 | 123 | empty |
| 4 | 629 | 0.82 | 0.86 | 85 | empty |
| 5 | 379 | 0.81 | 0.90 | 71 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3140 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2994 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 2915 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2780 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 92 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7SAA · Glycine and glutamate bound GluN1a-GluN2B NMDA receptors in non-active 1 conformation at… · the same entry in another collection · chain C against C, TM-score 1.00
- P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P35439
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 7SAA · PDBe 7SAA · UniProt P35439 · UniProt Q00960
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