MolNFT v1 · #128338 · protein
Crystal structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H3K9AC/K14AC)
5NND · Bromodomain-containing protein 4: “Crystal structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide…”. X-ray diffraction, 2 pockets (best druggability 0.52). MolNFT v1 #128338 on GenesisL1…
- PDB
- 5NND
- Type
- protein
- Length
- 267 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4; Histone H3
- UniProt
- O60885, Q5TEC6
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 4 | protein | 124 | 56% helix, 0% strand | O60885 |
| D | Histone H3 | protein | 10 | 30% helix, 0% strand | Q5TEC6 |
| E | Histone H3 | protein | 9 | 0% helix, 0% strand | Q5TEC6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.52 | 0.75 | 32 | empty |
| 2 | 53 | 0.38 | 0.81 | 13 | empty |
Interfaces
4 interfaces between chains.
- B–E · 481 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 477 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 197 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (acetylation, phosphorylation).
Compared structures
- 5NND · Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated… · the same entry in another collection · chain E against E, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain E against A, TM-score 0.51
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 Q5TEC6
- Elsewhere: RCSB PDB 5NND · PDBe 5NND · UniProt O60885 · UniProt Q5TEC6
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