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N-terminal bromodomain of human BRD2 with 5 ethyl-3-methyl- 4-phenyl-1,2-oxazole
Analyse N-terminal bromodomain of human BRD2 with 5 ethyl-3-methyl- 4-phenyl-1,2-oxazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A9O
- Type
- protein
- Length
- 330 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain containing 2
- UniProt
- P25440
- Ligands
- A9O, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain containing 2 | protein | 115 | 61% helix, 2% strand | P25440 |
| B | Bromodomain containing 2 | protein | 108 | 61% helix, 0% strand | P25440 |
| C | Bromodomain containing 2 | protein | 107 | 63% helix, 0% strand | P25440 |
Ligands and binding sites
- A9O · 5-ethyl-3-methyl-4-phenyl-1,2-oxazole · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.75 | 0.88 | 34 | A9O |
| 2 | 141 | 0.52 | 0.79 | 22 | A9O |
| 3 | 112 | 0.52 | 0.81 | 19 | A9O |
| 4 | 68 | 0.36 | 0.77 | 18 | empty |
| 5 | 50 | 0.31 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1104 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 145 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4A9O · N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5 ethyl-3-methyl-4-phenyl-1, 2-oxazole · 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 4A9O · PDBe 4A9O · UniProt P25440
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