Research workbench
First bromodomain (BD1) from candida albicans BDF1 in the unbound form
Analyse First bromodomain (BD1) from candida albicans BDF1 in the unbound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N15
- Type
- protein
- Length
- 529 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing factor 1
- UniProt
- Q5A4W8
- Ligands
- IOD
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing factor 1 | protein | 137 | 53% helix, 0% strand | Q5A4W8 |
| B | Bromodomain-containing factor 1 | protein | 132 | 58% helix, 0% strand | Q5A4W8 |
| C | Bromodomain-containing factor 1 | protein | 130 | 59% helix, 0% strand | Q5A4W8 |
| D | Bromodomain-containing factor 1 | protein | 130 | 55% helix, 0% strand | Q5A4W8 |
Ligands and binding sites
- IOD · Iodide ion · ion · 23 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.73 | 0.79 | 74 | IOD |
| 2 | 150 | 0.64 | 0.86 | 31 | IOD |
| 3 | 311 | 0.57 | 0.76 | 33 | empty |
| 4 | 124 | 0.55 | 0.82 | 28 | empty |
| 5 | 51 | 0.55 | 0.90 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 519 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 202 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 101 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5N15 · First Bromodomain (BD1) from Candida albicans Bdf1 in the unbound form · 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 D 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 5N15 · PDBe 5N15 · UniProt Q5A4W8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.