MolNFT v1 · #106735 · protein
C. elegans glutamate-gated chloride channel (glucl) in complex with Fab and popc in a lipid-modulated conformation
4TNW · Avermectin-sensitive glutamate-gated chloride channel glucl…: “C. elegans glutamate-gated chloride channel (glucl) in complex with Fab and popc in a lipid-modulated…”. X-ray diffraction, 3 ligands (POV, NAG, CL), 20 pockets (best…
- PDB
- 4TNW
- Type
- protein
- Length
- 7,746 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
- POV, NAG, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Avermectin-sensitive glutamate-gated chloride channel glucl alpha | protein | 342 | 34% helix, 30% strand | G5EBR3 |
| B | Avermectin-sensitive glutamate-gated chloride channel glucl alpha | protein | 341 | 34% helix, 30% strand | G5EBR3 |
| C, D, E, P, Q, R, S, T | Avermectin-sensitive glutamate-gated chloride channel glucl alpha | protein | 340 | 34% helix, 30% strand | G5EBR3 |
| F, U, Y | Mouse monoclonal Fab fragment, heavy chain | protein | 221 | 7% helix, 47% strand | — |
| G, I, J | Mouse monoclonal Fab fragment, heavy chain | protein | 222 | 7% helix, 45% strand | — |
| H | Mouse monoclonal Fab fragment, heavy chain | protein | 223 | 7% helix, 51% strand | — |
| K, M | Mouse monoclonal Fab fragment, light chain | protein | 210 | 4% helix, 52% strand | — |
| L, N, O, g, h | Mouse monoclonal Fab fragment, light chain | protein | 211 | 8% helix, 54% strand | — |
| V, W, X | Mouse monoclonal Fab fragment, heavy chain | protein | 224 | 5% helix, 49% strand | — |
| Z, f | Mouse monoclonal Fab fragment, light chain | protein | 215 | 7% helix, 52% strand | — |
| i | Mouse monoclonal Fab fragment, light chain | protein | 214 | 7% helix, 53% strand | — |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 7 copies · chains A, E, D, P, T, Q, R, S
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E, P, Q, S, T
- CL · Chloride ion · ion · 2 copies · chains Q, S
- LMT · Dodecyl-beta-D-maltoside · additive · 7 copies · chains B, C, D, E, P, S, T
- GOL · Glycerol · additive · chains A, 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 | 653 | 0.81 | 0.85 | 63 | empty |
| 2 | 632 | 0.80 | 0.85 | 64 | empty |
| 3 | 717 | 0.80 | 0.84 | 66 | empty |
| 4 | 635 | 0.80 | 0.85 | 64 | empty |
| 5 | 718 | 0.79 | 0.84 | 63 | empty |
Interfaces
51 interfaces between chains.
- B–C · 2414 Ų buried · 23 hydrogen bonds · protein-protein
- Q–R · 2396 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2377 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 2357 Ų buried · 19 hydrogen bonds · protein-protein
- P–Q · 2357 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4TNW · C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab and POPC in a… · the same entry in another collection · chain L against L, 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 4TNW · PDBe 4TNW · UniProt G5EBR3
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