Research workbench
Crystal structure of BRD4 bromodomain 1 in complex with acetylated rel peptide
Analyse Crystal structure of BRD4 bromodomain 1 in complex with acetylated rel peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KV1
- Type
- protein
- Length
- 268 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4; Rel peptide
- UniProt
- O60885, Q04206
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 128 | 52% helix, 0% strand | O60885 |
| C, D | Rel peptide | protein | 7 | 43% helix, 0% strand | Q04206 |
| B | Bromodomain-containing protein 4 | protein | 126 | 53% helix, 0% strand | O60885 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.61 | 0.77 | 40 | empty |
| 2 | 50 | 0.44 | 0.84 | 11 | empty |
| 3 | 130 | 0.41 | 0.75 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–C · 555 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 495 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 290 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 4KV1 · Crystal Structure of Brd4 Bromodomain 1 in Complex with Acetylated Rel Peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q04206 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04206) · a predicted model of the same protein · chain C against A, TM-score 0.62
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 O60885
- Every structure of UniProt Q04206
- Elsewhere: RCSB PDB 4KV1 · PDBe 4KV1 · UniProt O60885 · UniProt Q04206
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