Research workbench
Crystal structure of the second bromodomain H395R mutant of human BRD3
Analyse Crystal structure of the second bromodomain H395R mutant of human BRD3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HFR
- Type
- protein
- Length
- 438 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 3
- UniProt
- Q15059
- Ligands
- NO3
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 3 | protein | 110 | 71% helix, 0% strand | Q15059 |
| C, D | Bromodomain-containing protein 3 | protein | 109 | 70% helix, 0% strand | Q15059 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.76 | 0.80 | 78 | EDO |
| 2 | 268 | 0.59 | 0.79 | 26 | empty |
| 3 | 260 | 0.58 | 0.78 | 28 | empty |
| 4 | 404 | 0.57 | 0.74 | 36 | empty |
| 5 | 116 | 0.51 | 0.80 | 18 | NO3 |
Interfaces
5 interfaces between chains.
- B–D · 746 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 746 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 495 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 491 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HFR · Crystal structure of the second bromodomain H395R mutant of human BRD3 · 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 5HFR · PDBe 5HFR · UniProt Q15059
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