MolNFT v1 · #34940 · protein

Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide

2DVS · Bromodomain-containing protein 2: “Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4…”. X-ray diffraction, 1 ligand (ALY), 7 pockets (best druggability 0.65). MolNFT v1…

PDB: 2DVS
Type: protein
Length: 333 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: ALY
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	114	61% helix, 0% strand	P25440
B	Bromodomain-containing protein 2	protein	112	63% helix, 0% strand	P25440
C	Bromodomain-containing protein 2	protein	107	66% helix, 0% strand	P25440

Ligands and binding sites

ALY · N(6)-acetyllysine · ligand · 2 copies · chains A, B

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	164	0.65	0.86	33	empty
2	109	0.51	0.81	18	ALY
3	93	0.48	0.81	21	ALY
4	67	0.44	0.82	14	empty
5	62	0.37	0.79	16	empty

Interfaces

3 interfaces between chains.

A–B · 1124 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 552 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 86 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 modified (engineered).

Compared structures

2DVS · Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P25440
Elsewhere: RCSB PDB 2DVS · PDBe 2DVS · UniProt P25440

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