Research workbench
A closed pore conformation of a pentameic ligand-gated ion channel with additional N-terminal domain
Analyse A closed pore conformation of a pentameic ligand-gated ion channel with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V4S
- Type
- protein
- Length
- 2,941 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NEUR_CHAN_LBD domain-containing protein
- UniProt
- V4JF97
- Ligands
- NA, CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NEUR_CHAN_LBD domain-containing protein | protein | 585 | 24% helix, 39% strand | V4JF97 |
| E, D | NEUR_CHAN_LBD domain-containing protein | protein | 591 | 24% helix, 39% strand | V4JF97 |
| C | NEUR_CHAN_LBD domain-containing protein | protein | 588 | 24% helix, 39% strand | V4JF97 |
| B | NEUR_CHAN_LBD domain-containing protein | protein | 586 | 24% helix, 39% strand | V4JF97 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains A, E, D, C, B
- CA · Calcium ion · metal · 5 copies · chains A, B, E, D, C
- CL · Chloride ion · ion · 5 copies · chains A, E, D, C, B
- LMT · Dodecyl-beta-D-maltoside · additive · 10 copies · chains A, B, E, D, C
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 | 502 | 0.85 | 0.91 | 45 | NA |
| 2 | 90 | 0.76 | 0.97 | 20 | empty |
| 3 | 903 | 0.76 | 0.79 | 98 | empty |
| 4 | 834 | 0.76 | 0.80 | 93 | empty |
| 5 | 829 | 0.75 | 0.80 | 98 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3180 Ų buried · 26 hydrogen bonds · protein-protein
- D–C · 3125 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 3061 Ų buried · 21 hydrogen bonds · protein-protein
- E–D · 3057 Ų buried · 21 hydrogen bonds · protein-protein
- C–B · 3056 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6V4S · A Closed pore conformation of a Pentameic ligand-gated ion channel with additional… · 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 V4JF97
- Elsewhere: RCSB PDB 6V4S · PDBe 6V4S · UniProt V4JF97
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