MolNFT v1 · #146075 · protein
The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 19
6D6P · Transcriptional activator protein lasr: “The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 19”. X-ray diffraction, 1 ligand (FY1), 7 pockets (best druggability 0.83). MolNFT v1 #146075 on…
- PDB
- 6D6P
- 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
- FY1
- Pockets
- 7 · best druggability 0.83
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 | 48% helix, 18% strand | P25084 |
| B | Transcriptional activator protein lasr | protein | 163 | 52% helix, 18% strand | P25084 |
| C, D | Transcriptional activator protein lasr | protein | 166 | 54% helix, 16% strand | P25084 |
Ligands and binding sites
- FY1 · N-{[3,5-dibromo-2-(methoxymethoxy)phenyl]methyl}-2-nitrobenzamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.83 | 0.86 | 97 | FY1 |
| 2 | 299 | 0.77 | 0.88 | 38 | FY1 |
| 3 | 476 | 0.76 | 0.84 | 65 | FY1 |
| 4 | 222 | 0.47 | 0.73 | 30 | empty |
| 5 | 84 | 0.37 | 0.76 | 12 | empty |
Interfaces
4 interfaces between chains.
- C–D · 940 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 932 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 353 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 286 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6D6P · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 19 · the same entry in another collection · chain C against C, 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 0.97
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 6D6P · PDBe 6D6P · UniProt P25084
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