Research workbench
Crystal structure of the second bromodomain (BD2) of human brdt bound to bromosporine
Analyse Crystal structure of the second bromodomain (BD2) of human brdt bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LEL
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain testis-specific protein
- UniProt
- Q58F21
- Ligands
- BMF
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bromodomain testis-specific protein | protein | 114 | 69% helix, 0% strand | Q58F21 |
Ligands and binding sites
- BMF · Bromosporine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.72 | 0.83 | 44 | BMF |
| 2 | 566 | 0.71 | 0.79 | 59 | BMF |
| 3 | 475 | 0.58 | 0.73 | 43 | empty |
| 4 | 233 | 0.57 | 0.78 | 34 | BMF |
| 5 | 115 | 0.50 | 0.80 | 21 | BMF |
Interfaces
5 interfaces between chains.
- A–C · 455 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 438 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 298 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 70 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7LEL · Crystal structure of the second bromodomain (BD2) of human BRDT bound to Bromosporine · the same entry in another collection · chain D against D, TM-score 1.00
- Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q58F21
- Elsewhere: RCSB PDB 7LEL · PDBe 7LEL · UniProt Q58F21
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