Research workbench
Cryo-EM structure of GLUN1/GLUN2B NMDA receptor in the GLUTAMATE/GLYCINE-bound conformation
Analyse Cryo-EM structure of GLUN1/GLUN2B NMDA receptor in the GLUTAMATE/GLYCINE-bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IOU
- Type
- protein
- Length
- 3,200 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-methyl-D-aspartate receptor subunit NR1-8A; Ionotropic glutamate receptor subunit NR2B
- UniProt
- C0KD18, A7XY94
- Ligands
- GLY, GLU
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | N-methyl-D-aspartate receptor subunit NR1-8A | protein | 803 | 35% helix, 16% strand | C0KD18 |
| B, D | Ionotropic glutamate receptor subunit NR2B | protein | 797 | 34% helix, 17% strand | A7XY94 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, C
- GLU · Glutamic acid · ligand · 2 copies · chains B, 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 | 760 | 0.80 | 0.84 | 104 | empty |
| 2 | 442 | 0.78 | 0.87 | 71 | empty |
| 3 | 428 | 0.78 | 0.87 | 74 | empty |
| 4 | 708 | 0.76 | 0.82 | 81 | empty |
| 5 | 547 | 0.76 | 0.83 | 95 | empty |
Interfaces
5 interfaces between chains.
- C–D · 810 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 773 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 686 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 662 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 169 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IOU · Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine-bound… · the same entry in another collection · chain D against D, TM-score 1.00
- A7XY94 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (A7XY94) · 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 C0KD18
- Every structure of UniProt A7XY94
- Elsewhere: RCSB PDB 5IOU · PDBe 5IOU · UniProt C0KD18 · UniProt A7XY94
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.