MolNFT v1 · #146062 · protein
The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 12
6D6C · Transcriptional activator protein lasr: “The structure of ligand binding domain of lasr in complex with tp-1 homolog, compound 12”. X-ray diffraction, 2 ligands (FYD, HIS), 20 pockets (best druggability 0.82). MolNFT v1 #146062 on…
- PDB
- 6D6C
- Type
- protein
- Length
- 1,965 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator protein lasr
- UniProt
- P25084
- Ligands
- FYD, HIS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Transcriptional activator protein lasr | protein | 165 | 56% helix, 18% strand | P25084 |
| B, D | Transcriptional activator protein lasr | protein | 166 | 57% helix, 17% strand | P25084 |
| C | Transcriptional activator protein lasr | protein | 164 | 54% helix, 16% strand | P25084 |
| F | Transcriptional activator protein lasr | protein | 167 | 56% helix, 16% strand | P25084 |
| G, I | Transcriptional activator protein lasr | protein | 162 | 54% helix, 17% strand | P25084 |
| H | Transcriptional activator protein lasr | protein | 158 | 56% helix, 18% strand | P25084 |
| J | Transcriptional activator protein lasr | protein | 162 | 53% helix, 18% strand | P25084 |
| K | Transcriptional activator protein lasr | protein | 164 | 55% helix, 18% strand | P25084 |
| L | Transcriptional activator protein lasr | protein | 164 | 52% helix, 18% strand | P25084 |
Ligands and binding sites
- FYD · 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl) amino]methyl}phenyl 2-methoxybenzoate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- HIS · Histidine · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.82 | 0.94 | 36 | FYD |
| 2 | 252 | 0.81 | 0.93 | 38 | FYD |
| 3 | 221 | 0.81 | 0.94 | 31 | FYD |
| 4 | 231 | 0.81 | 0.93 | 32 | FYD |
| 5 | 228 | 0.80 | 0.93 | 34 | FYD |
Interfaces
16 interfaces between chains.
- A–C · 957 Ų buried · 12 hydrogen bonds · protein-protein
- D–L · 954 Ų buried · 12 hydrogen bonds · protein-protein
- H–J · 935 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 928 Ų buried · 12 hydrogen bonds · protein-protein
- F–K · 921 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6D6C · The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 12 · the same entry in another collection · chain E against E, TM-score 1.00
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 6D6C · PDBe 6D6C · UniProt P25084
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