Research workbench
Crystal structure analysis of the N-terminal bromodomain of human BRD2
Analyse Crystal structure analysis of the N-terminal bromodomain of human BRD2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X0J
- 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
- Pockets
- 8 · best druggability 0.66
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 | 62% 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
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.66 | 0.87 | 34 | DTT |
| 2 | 109 | 0.52 | 0.81 | 17 | DTT |
| 3 | 95 | 0.49 | 0.81 | 20 | DTT |
| 4 | 74 | 0.45 | 0.81 | 20 | empty |
| 5 | 55 | 0.38 | 0.80 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1088 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 541 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 1X0J · Crystal structure analysis of the N-terminal bromodomain of human Brd2 · 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 1X0J · PDBe 1X0J · UniProt P25440
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