Research workbench
Crystal structure of the NMDA receptor GLUN3A ligand binding domain apo state
Analyse Crystal structure of the NMDA receptor GLUN3A ligand binding domain apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KCD
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 3A
- UniProt
- Q9R1M7
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 3A | protein | 290 | 34% helix, 24% strand | Q9R1M7 |
| B | Glutamate receptor ionotropic, NMDA 3A | protein | 291 | 36% helix, 24% strand | Q9R1M7 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.58 | 0.77 | 38 | empty |
| 2 | 159 | 0.54 | 0.80 | 33 | empty |
| 3 | 154 | 0.54 | 0.80 | 35 | empty |
| 4 | 329 | 0.53 | 0.74 | 38 | GOL |
Interfaces
1 interface between chains.
- A–B · 534 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4KCD · Crystal Structure of the NMDA Receptor GluN3A Ligand Binding Domain Apo State · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R1M7 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 3A (Q9R1M7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9R1M7
- Elsewhere: RCSB PDB 4KCD · PDBe 4KCD · UniProt Q9R1M7
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