MolNFT v1 · #35177 · protein
Crystal structure of the human BRD2 second bromodomain in complexed with the acetylated histone H4 peptide
2E3K · Bromodomain-containing protein 2: “Crystal structure of the human BRD2 second bromodomain in complexed with the acetylated histone H4 peptide”. X-ray diffraction, 7 pockets (best druggability 0.59). MolNFT v1 #35177 on GenesisL1: 3D…
- 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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