MolNFT v1 · #114147 · protein
Activation of NMDA receptors and the mechanism of inhibition by ifenprodil
5B3J · NMDA glutamate receptor subunit: “Activation of NMDA receptors and the mechanism of inhibition by ifenprodil”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.75). MolNFT v1 #114147 on GenesisL1: 3D structure…
- PDB
- 5B3J
- Type
- protein
- Length
- 2,203 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NMDA glutamate receptor subunit; Glutamate receptor ionotropic, NMDA 2B; Fab, heavy…
- UniProt
- Q91977, Q00960
- Ligands
- NA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NMDA glutamate receptor subunit | protein | 347 | 36% helix, 23% strand | Q91977 |
| B | NMDA glutamate receptor subunit | protein | 338 | 37% helix, 20% strand | Q91977 |
| C | Glutamate receptor ionotropic, NMDA 2B | protein | 335 | 33% helix, 23% strand | Q00960 |
| E | Fab, heavy chain | protein | 215 | 1% helix, 52% strand | — |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 329 | 34% helix, 23% strand | Q00960 |
| F | Fab, light chain | protein | 211 | 7% helix, 53% strand | — |
| H | Fab, heavy chain | protein | 216 | 3% helix, 51% strand | — |
| L | Fab, light chain | protein | 212 | 7% helix, 52% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.75 | 0.77 | 88 | empty |
| 2 | 1100 | 0.74 | 0.77 | 94 | NA |
| 3 | 1045 | 0.73 | 0.76 | 123 | empty |
| 4 | 783 | 0.70 | 0.76 | 113 | empty |
| 5 | 333 | 0.61 | 0.78 | 48 | empty |
Interfaces
13 interfaces between chains.
- H–L · 1761 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1721 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1087 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1018 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 712 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5B3J · Activation of NMDA receptors and the mechanism of inhibition by ifenprodil · the same entry in another collection · chain L against L, TM-score 1.00
- Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain C 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 Q91977
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 5B3J · PDBe 5B3J · UniProt Q91977 · UniProt Q00960
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