MolNFT v1 · #146060 · protein
The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 10
6D6A · Transcriptional activator protein lasr: “The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 10”. X-ray diffraction, 1 ligand (FXD), 17 pockets (best druggability 0.82). MolNFT v1 #146060 on…
- PDB
- 6D6A
- Type
- protein
- Length
- 1,325 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator protein lasr
- UniProt
- P25084
- Ligands
- FXD
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 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, E | Transcriptional activator protein lasr | protein | 165 | 53% helix, 17% strand | P25084 |
| F | Transcriptional activator protein lasr | protein | 167 | 55% helix, 16% strand | P25084 |
| G | Transcriptional activator protein lasr | protein | 164 | 54% helix, 18% strand | P25084 |
Ligands and binding sites
- FXD · 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl) amino]methyl}phenyl benzoate · 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
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.82 | 0.94 | 32 | FXD |
| 2 | 213 | 0.81 | 0.94 | 31 | FXD |
| 3 | 219 | 0.81 | 0.94 | 33 | FXD |
| 4 | 250 | 0.80 | 0.92 | 36 | FXD |
| 5 | 229 | 0.80 | 0.93 | 32 | FXD |
Interfaces
7 interfaces between chains.
- E–F · 940 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 931 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 923 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 893 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 393 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6D6A · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 10 · the same entry in another collection · chain E against E, TM-score 1.00
- P25084 · AlphaFold monomer V2.0 prediction for transcriptional activator protein lasr (P25084) · a predicted model of the same protein · chain G 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 6D6A · PDBe 6D6A · UniProt P25084
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