MolNFT v1 · #146074 · protein
The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 17
6D6O · Transcriptional activator protein lasr: “The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 17”. X-ray diffraction, 1 ligand (FX7), 8 pockets (best druggability 0.82). MolNFT v1 #146074 on…
- PDB
- 6D6O
- Type
- protein
- Length
- 660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator protein lasr
- UniProt
- P25084
- Ligands
- FX7
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional activator protein lasr | protein | 165 | 49% helix, 16% strand | P25084 |
| B | Transcriptional activator protein lasr | protein | 163 | 50% helix, 18% strand | P25084 |
| C, D | Transcriptional activator protein lasr | protein | 166 | 54% helix, 16% strand | P25084 |
Ligands and binding sites
- FX7 · 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl) amino]methyl}phenyl octanoate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.82 | 0.86 | 94 | FX7 |
| 2 | 277 | 0.78 | 0.90 | 36 | FX7 |
| 3 | 259 | 0.76 | 0.89 | 36 | FX7 |
| 4 | 181 | 0.48 | 0.76 | 31 | empty |
| 5 | 213 | 0.46 | 0.73 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 937 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 923 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 364 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6D6O · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 17 · 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 B against A, TM-score 0.97
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 6D6O · PDBe 6D6O · UniProt P25084
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