Research workbench
Crystal structure of the methylene blue-bound form of the multi-drug binding transcriptional repressor cgmr
Analyse Crystal structure of the methylene blue-bound form of the multi-drug binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YVE
- Type
- protein
- Length
- 347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator
- UniProt
- Q8NMG3
- Ligands
- MBT, CL
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator | protein | 175 | 73% helix, 0% strand | Q8NMG3 |
| B | Transcriptional regulator | protein | 172 | 76% helix, 0% strand | Q8NMG3 |
Ligands and binding sites
- MBT · 3,7-bis(dimethylamino)phenothiazin-5-ium · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 6 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 | 108 | 0.56 | 0.84 | 16 | empty |
| 2 | 156 | 0.55 | 0.80 | 24 | MBT |
| 3 | 104 | 0.51 | 0.82 | 23 | MBT |
| 4 | 69 | 0.34 | 0.76 | 13 | empty |
| 5 | 59 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1981 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2YVE · Crystal structure of the methylene blue-bound form of the multi-drug binding… · 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 Q8NMG3
- Elsewhere: RCSB PDB 2YVE · PDBe 2YVE · UniProt Q8NMG3
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