Research workbench
Three-dimensional structure of the quorum sensing protein trar bound to its autoinducer and to its target DNA
Analyse Three-dimensional structure of the quorum sensing protein trar bound to its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H0M
- Type
- protein + DNA
- Length
- 989 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator protein trar; 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP…
- UniProt
- P33905
- Ligands
- LAE
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional activator protein trar | protein | 230 | 49% helix, 14% strand | P33905 |
| B | Transcriptional activator protein trar | protein | 230 | 48% helix, 15% strand | P33905 |
| C | Transcriptional activator protein trar | protein | 228 | 51% helix, 14% strand | P33905 |
| D | Transcriptional activator protein trar | protein | 229 | 48% helix, 15% strand | P33905 |
| E, F, G, H | 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3' | dna | 18 | — | — |
Ligands and binding sites
- LAE · 3-oxo-octanoic acid (2-oxo-tetrahydro-furan-3-yl)-amide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.79 | 0.83 | 61 | empty |
| 2 | 104 | 0.79 | 0.98 | 22 | LAE |
| 3 | 614 | 0.78 | 0.84 | 52 | empty |
| 4 | 104 | 0.77 | 0.96 | 24 | LAE |
| 5 | 106 | 0.76 | 0.96 | 23 | LAE |
Interfaces
18 interfaces between chains.
- A–B · 1803 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1720 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 824 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- E–F · 822 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- B–C · 415 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 1H0M · Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer… · the same entry in another collection · chain H against H, TM-score 1.00
- P33905 · AlphaFold monomer V2.0 prediction for transcriptional activator protein trar (P33905) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P33905
- Elsewhere: RCSB PDB 1H0M · PDBe 1H0M · UniProt P33905
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