MolNFT v1 · #137091 · protein
Crystal structure of human glycine receptor alpha-3 bound to am-3607, glycine, and ivermectin
5VDH · Glycine receptor subunit alpha-3: “Crystal structure of human glycine receptor alpha-3 bound to am-3607, glycine, and ivermectin”. X-ray diffraction, 6 ligands (7C6, GLY, IVM), 20 pockets (best druggability 0.79). MolNFT v1 #137091…
- PDB
- 5VDH
- 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, IVM, NAG, ZN, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 36% 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 | 37% helix, 29% strand | O75311 |
| D | Glycine receptor subunit alpha-3 | protein | 343 | 36% helix, 29% 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.79 | 0.82 | 88 | 7C6 |
| 2 | 555 | 0.79 | 0.85 | 46 | CL |
| 3 | 437 | 0.71 | 0.82 | 46 | 7C6 |
| 4 | 428 | 0.71 | 0.82 | 43 | 7C6 |
| 5 | 404 | 0.71 | 0.82 | 47 | 7C6 |
Interfaces
5 interfaces between chains.
- B–C · 2391 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2378 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2376 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 2358 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2353 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5VDH · Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607, Glycine, and… · 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 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 5VDH · PDBe 5VDH · UniProt O75311
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