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Crystal structure of the human BRPF1 bromodomain in complex with a histone H2AK5AC peptide

Analyse Crystal structure of the human BRPF1 bromodomain in complex with a histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QYL
Type: protein
Length: 508 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peregrin; Histone H2A type 1
UniProt: P55201, P0C0S8
Ligands: SO4
Pockets: 7 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Peregrin	protein	117	62% helix, 0% strand	P55201
E, F, G, H	Histone H2A type 1	protein	10	0% helix, 0% strand	P0C0S8

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.59	0.78	41	empty
2	264	0.57	0.78	41	empty
3	53	0.38	0.81	17	empty
4	64	0.30	0.74	12	empty
5	64	0.29	0.74	12	empty

Interfaces

6 interfaces between chains.

B–C · 676 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 675 Å² buried · 8 hydrogen bonds · protein-protein
D–H · 568 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 525 Å² buried · 5 hydrogen bonds · protein-protein
C–G · 518 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (acetylation).

Compared structures

4QYL · Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide · the same entry in another collection · chain H against H, TM-score 1.00
P55201 · AlphaFold monomer V2.0 prediction for peregrin (P55201) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P0C0S8
Elsewhere: RCSB PDB 4QYL · PDBe 4QYL · UniProt P55201 · UniProt P0C0S8

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