Research workbench
Crystal structure of human glycine receptor alpha-3 bound to am-3607
Analyse Crystal structure of human glycine receptor alpha-3 bound to am-3607 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TIO
- Type
- protein
- Length
- 1,700 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit alpha-3
- UniProt
- O75311
- Ligands
- 7C6, GLY, NAG, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, E | Glycine receptor subunit alpha-3 | protein | 338 | 36% helix, 32% strand | O75311 |
| B | Glycine receptor subunit alpha-3 | protein | 343 | 36% helix, 31% strand | O75311 |
| D | Glycine receptor subunit alpha-3 | protein | 343 | 36% helix, 31% strand | O75311 |
Ligands and binding sites
- 7C6 · (3s,3as,9bs)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3A,5,9B-hexahydro-4H-pyrrolo[3,4-C][1, 6]naphthyridin-4-one · ligand · 5 copies · chains C, D, A, B, E
- GLY · Glycine · ligand · 5 copies · chains C, D, A, B, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- ZN · Zinc ion · metal · 5 copies · chains C, A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.80 | 0.81 | 125 | empty |
| 2 | 404 | 0.71 | 0.82 | 44 | 7C6 |
| 3 | 417 | 0.71 | 0.82 | 44 | 7C6 |
| 4 | 410 | 0.71 | 0.82 | 45 | 7C6 |
| 5 | 392 | 0.70 | 0.82 | 44 | 7C6 |
Interfaces
5 interfaces between chains.
- C–B · 2419 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2417 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2416 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 2387 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2387 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- O75311 · AlphaFold monomer V2.0 prediction for glycine receptor subunit alpha-3 (O75311) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O75311
- Elsewhere: RCSB PDB 5TIO · PDBe 5TIO · UniProt O75311
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