MolNFT v1 · #101038 · protein
Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and glutamate in PEG2000MME
4NF8 · Glutamate receptor ionotropic, NMDA 1: “Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and glutamate in PEG2000MME”. X-ray diffraction, 2 ligands (GLY, GLU), 6 pockets (best druggability 0.80).…
- PDB
- 4NF8
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2A
- UniProt
- P35439, Q00959
- Ligands
- GLY, GLU
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 285 | 31% helix, 27% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 280 | 34% helix, 26% strand | Q00959 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.80 | 0.81 | 113 | empty |
| 2 | 59 | 0.59 | 0.91 | 24 | GLU |
| 3 | 214 | 0.58 | 0.80 | 35 | empty |
| 4 | 88 | 0.56 | 0.86 | 24 | empty |
| 5 | 58 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1235 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4NF8 · Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00959 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q00959) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · 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 P35439
- Every structure of UniProt Q00959
- Elsewhere: RCSB PDB 4NF8 · PDBe 4NF8 · UniProt P35439 · UniProt Q00959
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