Research workbench
Structure of the human GLUN1/GLUN2A NMDA receptor in the GLYCINE/CPP bound state
Analyse Structure of the human GLUN1/GLUN2A NMDA receptor in the GLYCINE/CPP bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EOQ
- Type
- protein
- Length
- 3,144 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 2A; Glutamate receptor ionotropic, NMDA 1
- UniProt
- Q12879, Q05586
- Ligands
- 7RC, NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 36% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 2A | protein | 783 | 34% helix, 13% strand | Q12879 |
| B, D | Glutamate receptor ionotropic, NMDA 1 | protein | 789 | 38% helix, 15% strand | Q05586 |
Ligands and binding sites
- 7RC · (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
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 | 960 | 0.89 | 0.91 | 139 | empty |
| 2 | 944 | 0.85 | 0.87 | 98 | empty |
| 3 | 959 | 0.85 | 0.86 | 98 | empty |
| 4 | 424 | 0.82 | 0.89 | 53 | empty |
| 5 | 186 | 0.82 | 0.96 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3686 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 3680 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2619 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2615 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7EOQ · Structure of the human GluN1/GluN2A NMDA receptor in the glycine/CPP bound state · the same entry in another collection · chain A against A, TM-score 1.00
- Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q12879
- Every structure of UniProt Q05586
- Elsewhere: RCSB PDB 7EOQ · PDBe 7EOQ · UniProt Q12879 · UniProt Q05586
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