MolNFT v1 · #48678 · protein
Crystal structure of an anti-activation complex in bacterial quorum sensing
2Q0O · Probable transcriptional activator protein trar: “Crystal structure of an anti-activation complex in bacterial quorum sensing”. X-ray diffraction, 1 ligand (LAE), 6 pockets (best druggability 0.80). MolNFT v1 #48678 on GenesisL1: 3D…
- PDB
- 2Q0O
- Type
- protein
- Length
- 643 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable transcriptional activator protein trar; Probable transcriptional repressor tram
- UniProt
- P55407, P55408
- Ligands
- LAE
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable transcriptional activator protein trar | protein | 235 | 55% helix, 14% strand | P55407 |
| C | Probable transcriptional repressor tram | protein | 86 | 74% helix, 0% strand | P55408 |
| D | Probable transcriptional repressor tram | protein | 87 | 74% helix, 0% strand | P55408 |
Ligands and binding sites
- LAE · 3-oxo-octanoic acid (2-oxo-tetrahydro-furan-3-yl)-amide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.80 | 0.98 | 24 | LAE |
| 2 | 1075 | 0.78 | 0.79 | 96 | empty |
| 3 | 116 | 0.77 | 0.96 | 22 | LAE |
| 4 | 141 | 0.61 | 0.85 | 32 | empty |
| 5 | 92 | 0.48 | 0.81 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1734 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1180 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1159 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 222 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 140 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2Q0O · Crystal structure of an anti-activation complex in bacterial quorum sensing · the same entry in another collection · chain A against A, TM-score 1.00
- P55408 · AlphaFold monomer V2.0 prediction for probable transcriptional repressor tram (P55408) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P55407 · AlphaFold monomer V2.0 prediction for probable transcriptional activator protein trar… · a predicted model of the same protein · chain A against A, TM-score 0.72
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 P55407
- Every structure of UniProt P55408
- Elsewhere: RCSB PDB 2Q0O · PDBe 2Q0O · UniProt P55407 · UniProt P55408
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