Research workbench
BRD2-BD1 in complex with the cyclic peptide 3.1_3
Analyse BRD2-BD1 in complex with the cyclic peptide 3.1_3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U61
- Type
- protein
- Length
- 257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2; Cyclic peptide 3.1_3
- UniProt
- H0Y6K2
- Ligands
- ACE, ZN, NH2
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 118 | 59% helix, 2% strand | H0Y6K2 |
| B | Bromodomain-containing protein 2 | protein | 117 | 60% helix, 2% strand | H0Y6K2 |
| E, D | Cyclic peptide 3.1_3 | protein | 11 | 0% helix, 45% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, E, B, D
- ZN · Zinc ion · metal · 3 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.55 | 0.87 | 19 | empty |
| 2 | 73 | 0.38 | 0.77 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–D · 574 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 569 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 539 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).
Compared structures
- 6U61 · BRD2-BD1 in complex with the cyclic peptide 3.1_3 · the same entry in another collection · chain A against A, TM-score 1.00
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 H0Y6K2
- Elsewhere: RCSB PDB 6U61 · PDBe 6U61 · UniProt H0Y6K2
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