Research workbench
C. elegans glutamate-gated chloride channel (glucl) in complex with Fab, ivermectin and glutamate.
Analyse C. elegans glutamate-gated chloride channel (glucl) in complex with Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RIF
- Type
- protein
- Length
- 3,670 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avermectin-sensitive glutamate-gated chloride channel glucl alpha; Mouse monoclonal Fab…
- UniProt
- O17793
- Ligands
- GLU, IVM, NAG, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 10 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Avermectin-sensitive glutamate-gated chloride channel glucl alpha | protein | 340 | 35% helix, 31% strand | O17793 |
| C | Avermectin-sensitive glutamate-gated chloride channel glucl alpha | protein | 339 | 35% helix, 30% strand | O17793 |
| F | Mouse monoclonal Fab fragment, heavy chain | protein | 171 | 5% helix, 47% strand | — |
| G | Mouse monoclonal Fab fragment, heavy chain | protein | 214 | 8% helix, 50% strand | — |
| H | Mouse monoclonal Fab fragment, heavy chain | protein | 221 | 8% helix, 50% strand | — |
| I | Mouse monoclonal Fab fragment, heavy chain | protein | 192 | 5% helix, 49% strand | — |
| J | Mouse monoclonal Fab fragment, heavy chain | protein | 200 | 6% helix, 53% strand | — |
| K, L, M | Mouse monoclonal Fab fragment, light chain | protein | 210 | 8% helix, 53% strand | — |
| N | Mouse monoclonal Fab fragment, light chain | protein | 148 | 4% helix, 49% strand | — |
| O | Mouse monoclonal Fab fragment, light chain | protein | 195 | 8% helix, 47% strand | — |
Ligands and binding sites
- GLU · Glutamic acid · 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, E, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, C, E
- CL · Chloride ion · ion
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains A, B
- OCT · N-octane · additive · 3 copies · chains B, D, E
- UND · Undecane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.83 | 0.85 | 88 | CL |
| 2 | 553 | 0.78 | 0.85 | 60 | GLU |
| 3 | 513 | 0.78 | 0.85 | 53 | GLU |
| 4 | 566 | 0.77 | 0.84 | 57 | GLU |
| 5 | 519 | 0.77 | 0.85 | 54 | GLU |
Interfaces
25 interfaces between chains.
- B–C · 2453 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2428 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2400 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2394 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2391 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3RIF · C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and… · 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
- Every structure of UniProt O17793
- Elsewhere: RCSB PDB 3RIF · PDBe 3RIF · UniProt O17793
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