Research workbench
BRD4-BD2 in complex with the cyclic peptide 3.1_2_ACK7TOA
Analyse BRD4-BD2 in complex with the cyclic peptide 3.1_2_ACK7TOA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U8G
- Type
- protein
- Length
- 495 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4; Cyclic peptide 3.1_2_ACK7TOA
- UniProt
- O60885
- Ligands
- ACE, NH2
- Pockets
- 8 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 4 | protein | 126 | 52% helix, 0% strand | O60885 |
| C | Bromodomain-containing protein 4 | protein | 108 | 62% helix, 0% strand | O60885 |
| D | Bromodomain-containing protein 4 | protein | 107 | 61% helix, 0% strand | O60885 |
| E, F | Cyclic peptide 3.1_2_ACK7TOA | protein | 14 | 0% helix, 43% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains E, F
- NH2 · Amino group · ion · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.51 | 0.82 | 17 | empty |
| 2 | 93 | 0.50 | 0.82 | 19 | empty |
| 3 | 173 | 0.43 | 0.74 | 29 | empty |
| 4 | 76 | 0.32 | 0.74 | 11 | empty |
| 5 | 66 | 0.31 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–F · 618 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 613 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 347 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 155 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).
Compared structures
- 6U8G · BRD4-BD2 in complex with the cyclic peptide 3.1_2_AcK7toA · the same entry in another collection · chain F against F, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain C 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 O60885
- Elsewhere: RCSB PDB 6U8G · PDBe 6U8G · UniProt O60885
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