Research workbench
Crystal structure of BRD9 bromodomain bound to a crotonyllysine peptide
Analyse Crystal structure of BRD9 bromodomain bound to a crotonyllysine peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YYK
- Type
- protein
- Length
- 416 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 9; Histone H4
- UniProt
- Q9H8M2, P62805
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Bromodomain-containing protein 9 | protein | 101 | 61% helix, 0% strand | Q9H8M2 |
| C, F | Histone H4 | protein | 6 | 0% helix, 0% strand | P62805 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.59 | 0.85 | 25 | empty |
| 2 | 129 | 0.56 | 0.83 | 27 | empty |
Interfaces
7 interfaces between chains.
- A–D · 396 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 359 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 350 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 341 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 337 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4YYK · Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide · the same entry in another collection · chain F against F, TM-score 1.00
- Q9H8M2 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 9 (Q9H8M2) · a predicted model of the same protein · chain E 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 Q9H8M2
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 4YYK · PDBe 4YYK · UniProt Q9H8M2 · UniProt P62805
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