MolNFT v1 · #97390 · protein
Crystal structure of the NMDA receptor GLUN3A ligand binding domain apo state
4KCD · Glutamate receptor ionotropic, NMDA 3A: “Crystal structure of the NMDA receptor GLUN3A ligand binding domain apo state”. X-ray diffraction, 4 pockets (best druggability 0.58). MolNFT v1 #97390 on GenesisL1: 3D structure, binding…
- 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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