Research workbench
Crystal structure of the NMDA receptor GLUN1 ligand binding domain apo state
Analyse Crystal structure of the NMDA receptor GLUN1 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
- 4KCC
- Type
- protein
- Length
- 275 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1
- UniProt
- P35439
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 275 | 33% helix, 28% strand | P35439 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.63 | 0.77 | 48 | empty |
| 2 | 76 | 0.36 | 0.76 | 18 | empty |
| 3 | 56 | 0.30 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4KCC · Crystal Structure of the NMDA Receptor GluN1 Ligand Binding Domain Apo State · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.92
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 P35439
- Elsewhere: RCSB PDB 4KCC · PDBe 4KCC · UniProt P35439
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