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The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 11
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
- 6D6B
- Type
- protein
- Length
- 1,324 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator protein lasr
- UniProt
- P25084
- Ligands
- FXS
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, H | Transcriptional activator protein lasr | protein | 166 | 57% helix, 16% strand | P25084 |
| D | Transcriptional activator protein lasr | protein | 163 | 55% helix, 18% strand | P25084 |
| E | Transcriptional activator protein lasr | protein | 165 | 56% helix, 18% strand | P25084 |
| F | Transcriptional activator protein lasr | protein | 164 | 55% helix, 18% strand | P25084 |
| G | Transcriptional activator protein lasr | protein | 168 | 55% helix, 17% strand | P25084 |
Ligands and binding sites
- FXS · 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl) amino]methyl}phenyl 2-nitrobenzoate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.82 | 0.94 | 33 | FXS |
| 2 | 234 | 0.82 | 0.94 | 33 | FXS |
| 3 | 220 | 0.81 | 0.94 | 34 | FXS |
| 4 | 247 | 0.81 | 0.93 | 35 | FXS |
| 5 | 226 | 0.81 | 0.94 | 35 | FXS |
Interfaces
8 interfaces between chains.
- A–C · 939 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 937 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 928 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 912 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 395 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6D6B · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 11 · the same entry in another collection · chain H against H, TM-score 1.00
- P25084 · AlphaFold monomer V2.0 prediction for transcriptional activator protein lasr (P25084) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 6D6B · PDBe 6D6B · UniProt P25084
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