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Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic 5A-formylbicyclomycin (fb)
Analyse Structural mechanism of inhibition of the rho transcription termination factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XPR
- Type
- protein + RNA
- Length
- 2,459 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'; Rho transcription termination factor
- UniProt
- P22869
- Ligands
- AGS, FB, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, M, H, J, K, L | 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' | rna | 2 | — | — |
| A, B, C, D, F | Rho transcription termination factor | protein | 408 | 33% helix, 16% strand | P22869 |
| E | Rho transcription termination factor | protein | 407 | 32% helix, 19% strand | P22869 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- FB · 5A-formylbicyclomycin · ligand · 5 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.83 | 0.84 | 96 | MG, AGS, FB |
| 2 | 1171 | 0.82 | 0.83 | 97 | MG, AGS, FB |
| 3 | 986 | 0.81 | 0.83 | 72 | MG, AGS, FB |
| 4 | 1078 | 0.81 | 0.82 | 93 | MG, AGS, FB |
| 5 | 1083 | 0.79 | 0.80 | 86 | MG, AGS, FB |
Interfaces
12 interfaces between chains.
- A–B · 1673 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1627 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1616 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1595 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1584 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1XPR · Structural mechanism of inhibition of the Rho transcription termination factor by the… · the same entry in another collection · chain F against F, TM-score 1.00
- P22869 · AlphaFold monomer V2.0 prediction for methane monooxygenase component a alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.29
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 P22869
- Elsewhere: RCSB PDB 1XPR · PDBe 1XPR · UniProt P22869
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