MolNFT v1 · #118895 · protein
Crystal structure of the bromodomain of human BRPF1 in complex with H3K14AC histone peptide
5FFV · Peregrin: “Crystal structure of the bromodomain of human BRPF1 in complex with H3K14AC histone peptide”. X-ray diffraction, 2 pockets (best druggability 0.73). MolNFT v1 #118895 on GenesisL1: 3D structure, binding sites and pockets…
- 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
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