Research workbench
Second bromodomain from leishmania donovani LDBPK.091320 complexed with bromosporine
Analyse Second bromodomain from leishmania donovani LDBPK.091320 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TCK
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- E9BA17
- Ligands
- BMF, SX
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 139 | 61% helix, 0% strand | E9BA17 |
| B | Uncharacterized protein | protein | 137 | 61% helix, 0% strand | E9BA17 |
Ligands and binding sites
- BMF · Bromosporine · ligand · 2 copies · chains A, B
- SX · Sulfur oxide · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.82 | 0.86 | 59 | BMF, BME, SX |
Interfaces
1 interface between chains.
- A–B · 742 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct, covalent ligand).
Compared structures
- 5TCK · Second Bromodomain from Leishmania donovani LdBPK.091320 complexed with Bromosporine · 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 E9BA17
- Elsewhere: RCSB PDB 5TCK · PDBe 5TCK · UniProt E9BA17
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