MolNFT v1 · #105725 · protein
Calcium-activated chloride channel bestrophin-1, from chicken, in complex with Fab antibody fragments, chloride and calcium
4RDQ: “Calcium-activated chloride channel bestrophin-1, from chicken, in complex with Fab antibody fragments…”. X-ray diffraction, 4 ligands (C6N, CA, K), 20 pockets (best druggability 0.74). MolNFT v1 #105725 on GenesisL1: 3D structure…
- PDB
- 4RDQ
- Type
- protein
- Length
- 3,945 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bestrophin-1; Fab antibody fragment, light chain; Fab antibody fragment, heavy chain
- UniProt
- E1C3A0
- Ligands
- C6N, CA, K, CL
- Pockets
- 20 · best druggability 0.74
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 | protein | 366 | 63% helix, 1% strand | E1C3A0 |
| F, H, J, L, N | Fab antibody fragment, light chain | protein | 212 | 4% helix, 51% strand | — |
| G, I, K, M, O | Fab antibody fragment, heavy chain | protein | 211 | 6% helix, 53% strand | — |
Ligands and binding sites
- C6N · 6-cyclohexyl-2-(4-cyclohexylbutyl)-2-({[4-O-(alpha-D-glucopyranosyl)-beta-D-glucopyranosyl]oxy}methyl)hexyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 5 copies · chains A, B, I, C, K, D, M, E, O, G
- CA · Calcium ion · metal · 5 copies · chains A, E, B, C, D
- K · Potassium 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 | 826 | 0.74 | 0.78 | 126 | CL |
| 2 | 901 | 0.72 | 0.76 | 69 | empty |
| 3 | 540 | 0.68 | 0.78 | 36 | empty |
| 4 | 214 | 0.66 | 0.84 | 23 | CL |
| 5 | 219 | 0.64 | 0.83 | 19 | CL |
Interfaces
40 interfaces between chains.
- C–D · 5228 Ų buried · 55 hydrogen bonds · protein-protein
- A–E · 5222 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 5218 Ų buried · 56 hydrogen bonds · protein-protein
- D–E · 5216 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 5209 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide (disulfide).
Compared structures
- 4RDQ · Calcium-activated chloride channel bestrophin-1, from chicken, in complex with Fab… · the same entry in another collection · chain N against N, 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 4RDQ · PDBe 4RDQ · UniProt E1C3A0
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