MolNFT v1 · #50233 · protein
Crystal structure of the NR3A ligand binding core complex with D- serine at 1.45 ångström resolution
2RC8 · Glutamate [NMDA] receptor subunit 3A: “Crystal structure of the NR3A ligand binding core complex with D- serine at 1.45 ångström resolution”. X-ray diffraction, 2 ligands (DSN, CL), 2 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 2RC8
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate [NMDA] receptor subunit 3A
- UniProt
- Q9R1M7
- Ligands
- DSN, CL
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate [NMDA] receptor subunit 3A | protein | 284 | 37% helix, 24% strand | Q9R1M7 |
| B | Glutamate [NMDA] receptor subunit 3A | protein | 285 | 36% helix, 24% strand | Q9R1M7 |
Ligands and binding sites
- DSN · D-serine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.81 | 0.83 | 89 | CL |
| 2 | 61 | 0.37 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 784 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2RC8 · Crystal structure of the NR3A ligand binding core complex with D-serine at 1.45 Angstrom… · 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 B against A, TM-score 0.98
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 2RC8 · PDBe 2RC8 · UniProt Q9R1M7
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