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Crystal structure of the bromo domain 2 of human bromodomain containing protein 3 (BRD3)
Analyse Crystal structure of the bromo domain 2 of human bromodomain containing protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OO1
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 3
- UniProt
- Q15059
- Ligands
- NA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bromodomain-containing protein 3 | protein | 110 | 70% helix, 0% strand | Q15059 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, D, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B, C
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.80 | 0.84 | 87 | NA, EDO, 7PE |
| 2 | 290 | 0.58 | 0.77 | 35 | empty |
| 3 | 331 | 0.54 | 0.74 | 35 | empty |
| 4 | 116 | 0.51 | 0.81 | 19 | empty |
| 5 | 97 | 0.47 | 0.80 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–D · 759 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 737 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 427 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 416 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2OO1 · Crystal structure of the Bromo domain 2 of human Bromodomain containing protein 3 (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 A 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 2OO1 · PDBe 2OO1 · UniProt Q15059
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