MolNFT v1 · #127593 · protein
First bromodomain (BD1) from candida albicans BDF1 bound to a dibenzothiazepinone (compound 1)
5N16 · Bromodomain-containing factor 1: “First bromodomain (BD1) from candida albicans BDF1 bound to a dibenzothiazepinone (compound 1)”. X-ray diffraction, 2 ligands (8FN, NI), 5 pockets (best druggability 0.83). MolNFT v1 #127593 on…
- PDB
- 5N16
- Type
- protein
- Length
- 515 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing factor 1
- UniProt
- Q5A4W8
- Ligands
- 8FN, NI
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Bromodomain-containing factor 1 | protein | 129 | 54% helix, 0% strand | Q5A4W8 |
| B | Bromodomain-containing factor 1 | protein | 128 | 55% helix, 0% strand | Q5A4W8 |
Ligands and binding sites
- 8FN · 5-cyclopropyl-2-(5-pyrazin-2-yl-1,2,4-oxadiazol-3-yl) benzo[b][1,4]benzothiazepin-6-one · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 5 copies · chains A, C, B, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.83 | 0.83 | 91 | 8FN, GOL |
| 2 | 601 | 0.76 | 0.82 | 53 | 8FN |
| 3 | 148 | 0.65 | 0.87 | 22 | empty |
| 4 | 67 | 0.47 | 0.83 | 15 | empty |
| 5 | 58 | 0.32 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 448 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 413 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 383 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5N16 · First Bromodomain (BD1) from Candida albicans Bdf1 bound to a dibenzothiazepi (compound 1) · the same entry in another collection · chain D against D, TM-score 1.00
- Q5A4W8 · AlphaFold monomer V2.0 prediction for bromodomain-containing factor 1 (Q5A4W8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5A4W8
- Elsewhere: RCSB PDB 5N16 · PDBe 5N16 · UniProt Q5A4W8
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