Research workbench
Crystal structure of the human BRD2 second bromodomain in complexed with the acetylated histone H4 peptide
Analyse Crystal structure of the human BRD2 second bromodomain in complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E3K
- Type
- protein
- Length
- 463 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2; 15-mer peptide from histone H4
- UniProt
- P25440, P02309
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bromodomain-containing protein 2 | protein | 108 | 70% helix, 0% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 110 | 68% helix, 0% strand | P25440 |
| D | Bromodomain-containing protein 2 | protein | 109 | 71% helix, 0% strand | P25440 |
| Q | 15-mer peptide from histone H4 | protein | 15 | 0% helix, 7% strand | P02309 |
| R | 15-mer peptide from histone H4 | protein | 13 | 0% helix, 0% strand | P02309 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.59 | 0.76 | 36 | empty |
| 2 | 326 | 0.58 | 0.76 | 36 | empty |
| 3 | 376 | 0.57 | 0.75 | 36 | empty |
| 4 | 101 | 0.53 | 0.83 | 21 | empty |
| 5 | 67 | 0.34 | 0.76 | 14 | empty |
Interfaces
7 interfaces between chains.
- A–C · 806 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 784 Ų buried · 7 hydrogen bonds · protein-protein
- C–Q · 577 Ų buried · 9 hydrogen bonds · protein-protein
- B–Q · 466 Ų buried · 6 hydrogen bonds · protein-protein
- D–R · 354 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 2E3K · Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated… · the same entry in another collection · chain R against R, TM-score 1.00
- P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain R against A, TM-score 0.23
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
- Every structure of UniProt P02309
- Elsewhere: RCSB PDB 2E3K · PDBe 2E3K · UniProt P25440 · UniProt P02309
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