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Crystal structure of the first bromodomain (BD1) of human brdt bound to nc-II-153
Analyse Crystal structure of the first bromodomain (BD1) 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
- 7MRG
- Type
- protein
- Length
- 219 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain testis-specific protein
- UniProt
- Q58F21
- Ligands
- ZMM, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain testis-specific protein | protein | 108 | 68% helix, 0% strand | Q58F21 |
| B | Bromodomain testis-specific protein | protein | 111 | 64% helix, 0% strand | Q58F21 |
Ligands and binding sites
- ZMM · 2-methyl-4-[3-(2-oxopyrrolidin-1-yl)phenyl]isoquinolin-1(2H)-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.66 | 0.79 | 57 | empty |
| 2 | 89 | 0.50 | 0.82 | 18 | ZMM |
| 3 | 98 | 0.46 | 0.79 | 18 | ZMM |
| 4 | 54 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 716 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7MRG · Crystal structure of the first bromodomain (BD1) of human BRDT bound to NC-II-153 · the same entry in another collection · chain A against A, TM-score 1.00
- Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · 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 Q58F21
- Elsewhere: RCSB PDB 7MRG · PDBe 7MRG · UniProt Q58F21
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