Research workbench
Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide
Analyse Crystal structure analysis of the N-terminal bromodomain of human BRD2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DVS
- Type
- protein
- Length
- 333 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- ALY
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 114 | 61% helix, 0% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 112 | 63% helix, 0% strand | P25440 |
| C | Bromodomain-containing protein 2 | protein | 107 | 66% helix, 0% strand | P25440 |
Ligands and binding sites
- ALY · N(6)-acetyllysine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.65 | 0.86 | 33 | empty |
| 2 | 109 | 0.51 | 0.81 | 18 | ALY |
| 3 | 93 | 0.48 | 0.81 | 21 | ALY |
| 4 | 67 | 0.44 | 0.82 | 14 | empty |
| 5 | 62 | 0.37 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1124 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 2DVS · Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P25440
- Elsewhere: RCSB PDB 2DVS · PDBe 2DVS · UniProt P25440
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