MolNFT v1 · #137092 · protein
Crystal structure of human glycine receptor alpha-3 mutant N38Q bound to am-3607, glycine, and ivermectin
5VDI · Glycine receptor subunit alpha-3: “Crystal structure of human glycine receptor alpha-3 mutant N38Q bound to am-3607, glycine, and ivermectin”. X-ray diffraction, 4 ligands (7C6, GLY, IVM), 20 pockets (best druggability 0.81). MolNFT…
- PDB
- 5VDI
- Type
- protein
- Length
- 1,698 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, IVM, ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Glycine receptor subunit alpha-3 | protein | 338 | 37% helix, 30% strand | O75311 |
| B | Glycine receptor subunit alpha-3 | protein | 343 | 36% helix, 30% strand | O75311 |
| D | Glycine receptor subunit alpha-3 | protein | 341 | 37% 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
- IVM · (2ae,4e,5's,6s,6'r,7s,8e,11r,13r,15s,17ar,20r,20ar, 20BS)-6'-[(2S)-butan-2-yl]-20,20B-dihydroxy-5',6,8,19-tetramethyl-17-oxo-3',4',5',6,6',10,11,14,15,17,17A, 20,20A,20B-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacyclooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside · ligand · 5 copies · chains A, B, C, D, E
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.81 | 0.84 | 77 | empty |
| 2 | 845 | 0.76 | 0.80 | 96 | IVM |
| 3 | 424 | 0.71 | 0.82 | 47 | 7C6 |
| 4 | 354 | 0.71 | 0.83 | 42 | empty |
| 5 | 387 | 0.70 | 0.82 | 40 | 7C6 |
Interfaces
5 interfaces between chains.
- A–B · 2335 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2322 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2321 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2307 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 2292 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5VDI · Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607… · the same entry in another collection · chain D against D, 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 E 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 5VDI · PDBe 5VDI · UniProt O75311
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