Research workbench
Calcium-activated chloride channel bestrophin-1 (BEST1), triple mutant: I76A, F80A, F84A; in complex with an Fab antibody fragment, chloride, and calcium
Analyse Calcium-activated chloride channel bestrophin-1 (BEST1), triple mutant: I76A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T5N
- Type
- protein
- Length
- 3,945 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bestrophin-1 (BEST1); Fab antibody fragment, light chain (10D10); Fab antibody fragment…
- UniProt
- E1C3A0
- Ligands
- K, CA, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Bestrophin-1 (BEST1) | protein | 366 | 63% helix, 1% strand | E1C3A0 |
| F, H, J, L, N | Fab antibody fragment, light chain (10D10) | protein | 212 | 4% helix, 51% strand | — |
| G, I, K, M, O | Fab antibody fragment, heavy chain (10D10) | protein | 211 | 6% helix, 53% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, E, C, D
- CA · Calcium ion · metal · 5 copies · chains A, E, B, C, D
- CL · Chloride ion · ion · 15 copies · chains A, B, E, C, D
- GOL · Glycerol · additive · 5 copies · chains A, E, 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 | 794 | 0.72 | 0.78 | 60 | empty |
| 2 | 542 | 0.68 | 0.78 | 38 | empty |
| 3 | 50 | 0.68 | 0.96 | 14 | empty |
| 4 | 205 | 0.64 | 0.83 | 25 | CL |
| 5 | 215 | 0.63 | 0.83 | 23 | CL |
Interfaces
40 interfaces between chains.
- A–B · 5095 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 5087 Ų buried · 60 hydrogen bonds · protein-protein
- A–E · 5080 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 5080 Ų buried · 59 hydrogen bonds · protein-protein
- D–E · 5075 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide (disulfide).
Compared structures
- 5T5N · Calcium-activated chloride channel bestrophin-1 (BEST1), triple mutant: I76A, F80A, F84A… · 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 E1C3A0
- Elsewhere: RCSB PDB 5T5N · PDBe 5T5N · UniProt E1C3A0
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