Research workbench
Crystal structure of human glycine receptor alpha-3 mutant N38Q bound to am-3607
Analyse Crystal structure of human glycine receptor alpha-3 mutant N38Q 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
- 5TIN
- 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, ZN, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Glycine receptor subunit alpha-3 | protein | 338 | 36% helix, 30% strand | O75311 |
| B | Glycine receptor subunit alpha-3 | protein | 343 | 35% helix, 30% strand | O75311 |
| D | Glycine receptor subunit alpha-3 | protein | 343 | 35% helix, 30% 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 A, B, C, D, E
- GLY · Glycine · ligand · 5 copies · chains A, B, C, D, E
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D, E
- CL · Chloride ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.79 | 0.84 | 63 | CL |
| 2 | 442 | 0.74 | 0.84 | 69 | empty |
| 3 | 419 | 0.71 | 0.82 | 46 | 7C6 |
| 4 | 439 | 0.71 | 0.81 | 47 | 7C6 |
| 5 | 405 | 0.70 | 0.82 | 42 | 7C6 |
Interfaces
5 interfaces between chains.
- A–B · 2389 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2384 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2375 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2366 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 2337 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5TIN · Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607 · the same entry in another collection · chain E against E, TM-score 1.00
- O75311 · AlphaFold monomer V2.0 prediction for glycine receptor subunit alpha-3 (O75311) · a predicted model of the same protein · chain A 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 5TIN · PDBe 5TIN · UniProt O75311
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