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
- 2DVQ
- Type
- protein
- Length
- 356 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2; Histone H4
- UniProt
- P25440
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 114 | 62% helix, 0% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 112 | 63% helix, 1% strand | P25440 |
| C | Bromodomain-containing protein 2 | protein | 107 | 66% helix, 0% strand | P25440 |
| P | Histone H4 | protein | 8 | 0% helix, 0% strand | — |
| Q | Histone H4 | protein | 15 | 0% helix, 7% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.62 | 0.84 | 34 | empty |
| 2 | 66 | 0.46 | 0.83 | 17 | empty |
| 3 | 54 | 0.40 | 0.81 | 14 | empty |
| 4 | 84 | 0.34 | 0.75 | 22 | empty |
| 5 | 54 | 0.34 | 0.78 | 14 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1119 Ų buried · 14 hydrogen bonds · protein-protein
- B–Q · 804 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 2 hydrogen bonds · protein-protein
- A–P · 498 Ų buried · 10 hydrogen bonds · protein-protein
- A–Q · 294 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered, acetylation).
Compared structures
- 2DVQ · Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with… · the same entry in another collection · chain Q against Q, 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 2DVQ · PDBe 2DVQ · UniProt P25440
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.