Research workbench
Aplysia SLO1 with barium
Analyse Aplysia SLO1 with barium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RK6
- Type
- protein
- Length
- 3,564 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bk channel
- UniProt
- Q5QJC5
- Ligands
- PGW, BA, K
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bk channel | protein | 891 | 47% helix, 13% strand | Q5QJC5 |
Ligands and binding sites
- PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 16 copies · chains A, B, C, D
- BA · Barium ion · metal · 8 copies · chains A, B, C, D
- K · Potassium ion · metal · 3 copies · chains A, B, C, D
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 | 682 | 0.76 | 0.81 | 68 | empty |
| 2 | 78 | 0.74 | 0.98 | 21 | empty |
| 3 | 76 | 0.74 | 0.98 | 21 | empty |
| 4 | 73 | 0.74 | 0.98 | 20 | empty |
| 5 | 78 | 0.73 | 0.97 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1738 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1732 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1732 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1729 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RK6 · Aplysia Slo1 with Barium · 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 Q5QJC5
- Elsewhere: RCSB PDB 7RK6 · PDBe 7RK6 · UniProt Q5QJC5
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