Research workbench
Structure of alpha-1 glycine receptor by single particle electron cryo-microscopy, GLYCINE/IVERMECTIN-bound state
Analyse Structure of alpha-1 glycine receptor by single particle electron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JAF
- Type
- protein
- Length
- 1,710 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- Ligands
- IVM, NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycine receptor subunit ALPHAZ1 | protein | 342 | 37% helix, 27% strand | — |
Ligands and binding sites
- 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 · 10 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.83 | 0.83 | 84 | empty |
| 2 | 460 | 0.72 | 0.82 | 53 | empty |
| 3 | 559 | 0.71 | 0.80 | 62 | empty |
| 4 | 530 | 0.71 | 0.80 | 62 | empty |
| 5 | 534 | 0.71 | 0.80 | 60 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2276 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 2270 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 2253 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 2230 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 2195 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3JAF · Structure of alpha-1 glycine receptor by single particle electron cryo-microscopy… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3JAF · PDBe 3JAF
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