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Crystal structure of the second bromodomain of human BRD3 in complex with compound
Analyse Crystal structure of the second bromodomain of human BRD3 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A7C
- Type
- protein
- Length
- 441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- HOMO SAPIENS
- Molecule
- Bromodomain-containing protein 3
- UniProt
- Q15059
- Ligands
- 5D4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.9 · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 3 | protein | 112 | 68% helix, 0% strand | Q15059 |
| B | Bromodomain-containing protein 3 | protein | 111 | 68% helix, 0% strand | Q15059 |
| C, D | Bromodomain-containing protein 3 | protein | 109 | 70% helix, 0% strand | Q15059 |
Ligands and binding sites
- 5D4 · N-(6-acetamidohexyl)acetamide · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.74 | 0.80 | 60 | 5D4, EDO |
| 2 | 362 | 0.58 | 0.76 | 35 | empty |
| 3 | 374 | 0.57 | 0.75 | 36 | empty |
| 4 | 111 | 0.48 | 0.80 | 21 | 5D4 |
| 5 | 114 | 0.48 | 0.79 | 21 | 5D4 |
Interfaces
4 interfaces between chains.
- A–B · 755 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 741 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 521 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 72 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5A7C · Crystal structure of the second bromodomain of human BRD3 in complex with compound · the same entry in another collection · chain D against D, TM-score 1.00
- Q15059 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 3 (Q15059) · a predicted model of the same protein · chain C 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 Q15059
- Elsewhere: RCSB PDB 5A7C · PDBe 5A7C · UniProt Q15059
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