Research workbench
Crystal structure of the mycobacterium tuberculosis transcriptional repressor ETHR2 in complex with BDM41420
Analyse Crystal structure of the mycobacterium tuberculosis transcriptional repressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ICJ
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcriptional regulatory protein
- UniProt
- O53623
- Ligands
- 69Y
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable transcriptional regulatory protein | protein | 190 | 84% helix, 0% strand | O53623 |
| B | Probable transcriptional regulatory protein | protein | 186 | 85% helix, 0% strand | O53623 |
Ligands and binding sites
- 69Y · 4,4,4-trifluoro-1-(3-phenyl-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl)butan-1-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.82 | 0.96 | 36 | 69Y |
| 2 | 143 | 0.80 | 0.96 | 27 | 69Y |
| 3 | 93 | 0.76 | 0.97 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1463 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5ICJ · Crystal structure of the Mycobacterium tuberculosis transcriptional repressor EthR2 in… · 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 O53623
- Elsewhere: RCSB PDB 5ICJ · PDBe 5ICJ · UniProt O53623
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