MolNFT v1 · #34939 · protein

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

2DVR · Bromodomain-containing protein 2: “Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4…”. X-ray diffraction, 8 pockets (best druggability 0.65). MolNFT v1 #34939 on GenesisL1…

PDB: 2DVR
Type: protein
Length: 351 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2; Histone H4
UniProt: P25440
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 5 distinct chains · 58% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	114	62% helix, 1% strand	P25440
B	Bromodomain-containing protein 2	protein	112	63% helix, 1% strand	P25440
C	Bromodomain-containing protein 2	protein	107	60% helix, 0% strand	P25440
P	Histone H4	protein	8	0% helix, 13% strand	—
Q	Histone H4	protein	10	0% helix, 10% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	158	0.65	0.86	33	empty
2	70	0.45	0.82	18	empty
3	61	0.45	0.83	14	empty
4	66	0.36	0.78	16	empty
5	67	0.34	0.76	15	empty

Interfaces

8 interfaces between chains.

A–B · 1112 Å² buried · 10 hydrogen bonds · protein-protein
B–Q · 611 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 547 Å² buried · 3 hydrogen bonds · protein-protein
A–P · 517 Å² buried · 10 hydrogen bonds · protein-protein
A–Q · 169 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 23 modified (engineered, acetylation).

Compared structures

2DVR · Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with… · the same entry in another collection · chain Q against Q, 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 2DVR · PDBe 2DVR · UniProt P25440

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