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The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 13
Analyse The structure of ligand binding domain of lasr in complex with tp-1 homolog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D6D
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator protein lasr
- UniProt
- P25084
- Ligands
- FY7
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional activator protein lasr | protein | 162 | 54% helix, 17% strand | P25084 |
| B | Transcriptional activator protein lasr | protein | 164 | 50% helix, 18% strand | P25084 |
Ligands and binding sites
- FY7 · 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl) amino]methyl}phenyl 2-cyanobenzoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.81 | 0.95 | 29 | FY7 |
| 2 | 277 | 0.79 | 0.91 | 39 | FY7 |
| 3 | 179 | 0.48 | 0.76 | 31 | empty |
| 4 | 58 | 0.28 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 905 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6D6D · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 13 · the same entry in another collection · chain A against A, TM-score 1.00
- P25084 · AlphaFold monomer V2.0 prediction for transcriptional activator protein lasr (P25084) · a predicted model of the same protein · chain A 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 P25084
- Elsewhere: RCSB PDB 6D6D · PDBe 6D6D · UniProt P25084
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