MolNFT v1 · #106734 · protein
C. elegans glutamate-gated chloride channel (glucl) in complex with Fab in a non-conducting conformation
4TNV · Avermectin-sensitive glutamate-gated chloride channel glucl…: “C. elegans glutamate-gated chloride channel (glucl) in complex with Fab in a non-conducting conformation”. X-ray diffraction, 2 ligands (NAG, CL), 20 pockets (best…
- PDB
- 4TNV
- Type
- protein
- Length
- 7,719 residues
- Chains
- 30
- 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
- G5EBR3
- Ligands
- NAG, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, P, Q, R, S, T | Avermectin-sensitive glutamate-gated chloride channel glucl alpha | protein | 337 | 35% helix, 29% strand | G5EBR3 |
| F, I | Mouse monoclonal Fab fragment, heavy chain | protein | 222 | 0% helix, 48% strand | — |
| G, V, W, X | Mouse monoclonal Fab fragment, heavy chain | protein | 224 | 3% helix, 43% strand | — |
| H, J | Mouse monoclonal Fab fragment, heavy chain | protein | 223 | 3% helix, 48% strand | — |
| K | Mouse monoclonal Fab fragment, light chain | protein | 212 | 7% helix, 50% strand | — |
| L, N, O, g, h, M | Mouse monoclonal Fab fragment, light chain | protein | 211 | 7% helix, 49% strand | — |
| U, Y | Mouse monoclonal Fab fragment, heavy chain | protein | 221 | 0% helix, 46% strand | — |
| Z | Mouse monoclonal Fab fragment, light chain | protein | 215 | 5% helix, 49% strand | — |
| f, i | Mouse monoclonal Fab fragment, light chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E, P, Q, R, S, T
- CL · Chloride ion · ion · 2 copies · chains T
- LMT · Dodecyl-beta-D-maltoside · additive · 10 copies · chains A, B, C, D, E, P, Q, R, S, T
- FLC · Citrate anion · additive · 2 copies · chains A, C, P, T
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 | 621 | 0.82 | 0.87 | 75 | CL |
| 2 | 910 | 0.80 | 0.82 | 114 | empty |
| 3 | 645 | 0.80 | 0.85 | 67 | empty |
| 4 | 623 | 0.79 | 0.85 | 62 | empty |
| 5 | 660 | 0.79 | 0.84 | 62 | empty |
Interfaces
53 interfaces between chains.
- A–E · 2328 Ų buried · 17 hydrogen bonds · protein-protein
- S–T · 2266 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2266 Ų buried · 13 hydrogen bonds · protein-protein
- W–f · 2261 Ų buried · 18 hydrogen bonds · protein-protein
- Q–R · 2227 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4TNV · C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab in a… · the same entry in another collection · chain Z against Z, 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 G5EBR3
- Elsewhere: RCSB PDB 4TNV · PDBe 4TNV · UniProt G5EBR3
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