Research workbench
Crystal structure of the NR1 ligand binding core in complex with 5,7- dichlorokynurenic acid (dcka) at 1.90 ångströms resolution
Analyse Crystal structure of the NR1 ligand binding core in complex with 5,7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PBQ
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-methyl-D-aspartate receptor subunit 1
- UniProt
- P35439
- Ligands
- DK1
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-methyl-D-aspartate receptor subunit 1 | protein | 274 | 32% helix, 28% strand | P35439 |
| B | N-methyl-D-aspartate receptor subunit 1 | protein | 266 | 33% helix, 26% strand | — |
Ligands and binding sites
- DK1 · 5,7-dichloro-4-hydroxyquinoline-2-carboxylic acid · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.65 | 0.77 | 44 | DK1 |
| 2 | 414 | 0.65 | 0.78 | 37 | DK1 |
| 3 | 75 | 0.32 | 0.75 | 16 | empty |
| 4 | 59 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 65 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1PBQ · Crystal structure of the NR1 ligand binding core in complex with 5,7-dichlorokynurenic… · 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 1PBQ · PDBe 1PBQ · UniProt P35439
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