Research workbench
Ligand binding domain of metabotropoc glutamate receptor MGLUR5 complexed with glutamate
Analyse Ligand binding domain of metabotropoc glutamate receptor MGLUR5 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMK
- Type
- protein
- Length
- 877 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 5
- UniProt
- P41594
- Ligands
- GLU, NAG, MG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 5 | protein | 438 | 37% helix, 21% strand | P41594 |
| B | Metabotropic glutamate receptor 5 | protein | 439 | 37% helix, 20% strand | P41594 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.80 | 0.81 | 88 | empty |
| 2 | 235 | 0.56 | 0.78 | 36 | empty |
| 3 | 205 | 0.55 | 0.79 | 34 | empty |
| 4 | 145 | 0.52 | 0.80 | 23 | empty |
| 5 | 73 | 0.51 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 859 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3LMK · Ligand Binding Domain of Metabotropoc glutamate receptor mGluR5 complexed with glutamate · the same entry in another collection · chain A against A, TM-score 1.00
- P41594 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 5 (P41594) · a predicted model of the same protein · chain B 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 P41594
- Elsewhere: RCSB PDB 3LMK · PDBe 3LMK · UniProt P41594
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