Research workbench
Cryo-EM structure of GLUN1/GLUN2B NMDA receptor in the GLUTAMATE/GLYCINE/RO25-6981-bound conformation
Analyse Cryo-EM structure of GLUN1/GLUN2B NMDA receptor in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IOV
- Type
- protein
- Length
- 3,201 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, QEM, GLU
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 34% helix, 16% 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 | Ionotropic glutamate receptor subunit NR2B | protein | 798 | 34% helix, 16% strand | A7XY94 |
| D | Ionotropic glutamate receptor subunit NR2B | protein | 797 | 34% helix, 16% strand | A7XY94 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, C
- QEM · 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol · ligand · 2 copies · chains A, B, C, D
- 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 | 1120 | 0.83 | 0.84 | 143 | empty |
| 2 | 979 | 0.82 | 0.83 | 122 | empty |
| 3 | 611 | 0.79 | 0.85 | 74 | empty |
| 4 | 972 | 0.79 | 0.81 | 123 | empty |
| 5 | 597 | 0.78 | 0.84 | 88 | empty |
Interfaces
5 interfaces between chains.
- A–B · 830 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 804 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 641 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 595 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IOV · Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine/Ro25-6981-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 D against A, TM-score 0.93
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 5IOV · PDBe 5IOV · UniProt C0KD18 · UniProt A7XY94
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