Research workbench
Cryo-EM structure of GLUN1/GLUN2B NMDA receptor in the DCKA/D-apv- bound conformation, state 4
Analyse Cryo-EM structure of GLUN1/GLUN2B NMDA receptor in the DCKA/D-apv- bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IPS
- Type
- protein
- Length
- 2,545 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
- Pockets
- 20 · best druggability 0.71
Structure
electron microscopy · 4 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-methyl-D-aspartate receptor subunit NR1-8A | protein | 658 | 34% helix, 20% strand | C0KD18 |
| B | Ionotropic glutamate receptor subunit NR2B | protein | 633 | 31% helix, 20% strand | A7XY94 |
| C | N-methyl-D-aspartate receptor subunit NR1-8A | protein | 627 | 34% helix, 19% strand | C0KD18 |
| D | Ionotropic glutamate receptor subunit NR2B | protein | 627 | 32% helix, 19% strand | A7XY94 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.71 | 0.76 | 122 | empty |
| 2 | 804 | 0.70 | 0.77 | 99 | empty |
| 3 | 733 | 0.70 | 0.78 | 94 | empty |
| 4 | 630 | 0.69 | 0.79 | 88 | empty |
| 5 | 533 | 0.69 | 0.80 | 89 | empty |
Interfaces
2 interfaces between chains.
- A–B · 198 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 148 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5IPS · Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation… · the same entry in another collection · chain A against A, 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 0.65
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 5IPS · PDBe 5IPS · UniProt C0KD18 · UniProt A7XY94
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