Research workbench
Crystal structure of the NR1 ligand binding core in complex with D- serine at 1.45 ångströms resolution
Analyse Crystal structure of the NR1 ligand binding core in complex with D- serine at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PB8
- Type
- protein
- Length
- 282 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-methyl-D-aspartate receptor subunit 1
- UniProt
- P35439
- Ligands
- DSN
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-methyl-D-aspartate receptor subunit 1 | protein | 282 | 30% helix, 27% strand | P35439 |
Ligands and binding sites
- DSN · D-serine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.50 | 0.79 | 32 | empty |
| 2 | 85 | 0.38 | 0.77 | 22 | empty |
| 3 | 84 | 0.36 | 0.75 | 18 | empty |
| 4 | 53 | 0.29 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1PB8 · Crystal structure of the NR1 ligand binding core in complex with D-serine at 1.45… · 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 0.96
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
- Elsewhere: RCSB PDB 1PB8 · PDBe 1PB8 · UniProt P35439
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