Research workbench
Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2
Analyse Crystal structure of the N-terminus D161Y bromodomain mutant 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
- 5HEM
- Type
- protein
- Length
- 237 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- MG
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 121 | 55% helix, 2% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 116 | 58% helix, 2% strand | P25440 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
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 | 316 | 0.73 | 0.85 | 42 | ACT |
| 2 | 53 | 0.29 | 0.75 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 727 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5HEM · Crystal structure of the N-terminus D161Y bromodomain mutant 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 B against A, TM-score 0.99
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 5HEM · PDBe 5HEM · UniProt P25440
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