Research workbench
Crystal structure of the bromodomain of human BRPF1 in complex with H3K14AC histone peptide
Analyse Crystal structure of the bromodomain of human BRPF1 in complex with H3K14AC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FFV
- Type
- protein
- Length
- 235 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin; Histone H3
- UniProt
- P55201, K7EMV3
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peregrin | protein | 111 | 65% helix, 0% strand | P55201 |
| B | Peregrin | protein | 108 | 69% helix, 0% strand | P55201 |
| C, D | Histone H3 | protein | 8 | 0% helix, 0% strand | K7EMV3 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
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 | 554 | 0.73 | 0.81 | 59 | empty |
| 2 | 55 | 0.30 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 629 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 489 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 468 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 5FFV · Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone… · the same entry in another collection · chain A against A, TM-score 1.00
- P55201 · AlphaFold monomer V2.0 prediction for peregrin (P55201) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P55201
- Every structure of UniProt K7EMV3
- Elsewhere: RCSB PDB 5FFV · PDBe 5FFV · UniProt P55201 · UniProt K7EMV3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.