Research workbench
An open conformation of a pentameic ligand-gated ion channel with additional N-terminal domain
Analyse An open conformation of a pentameic ligand-gated ion channel with additional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V4A
- Type
- protein
- Length
- 2,955 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
- P3A
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NEUR_CHAN_LBD domain-containing protein | protein | 589 | 24% helix, 37% strand | V4JF97 |
| E, D | NEUR_CHAN_LBD domain-containing protein | protein | 592 | 24% helix, 36% strand | V4JF97 |
| C | NEUR_CHAN_LBD domain-containing protein | protein | 593 | 24% helix, 36% strand | V4JF97 |
Ligands and binding sites
- P3A · Phosphatidylglycerol-phosphoglycerol · ligand · 5 copies · chains A, B, E, D, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 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 | 1107 | 0.86 | 0.87 | 146 | empty |
| 2 | 1072 | 0.86 | 0.87 | 124 | empty |
| 3 | 861 | 0.85 | 0.87 | 113 | empty |
| 4 | 856 | 0.84 | 0.87 | 105 | empty |
| 5 | 1059 | 0.83 | 0.84 | 122 | empty |
Interfaces
5 interfaces between chains.
- D–C · 2441 Ų buried · 25 hydrogen bonds · protein-protein
- C–B · 2441 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 2416 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2370 Ų buried · 25 hydrogen bonds · protein-protein
- E–D · 2317 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6V4A · An open conformation of a Pentameic ligand-gated ion channel with additional N-terminal… · 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 6V4A · PDBe 6V4A · UniProt V4JF97
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